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Shin S, Han MJ, Jedrychowski MP, Zhang Z, Shokat KM, Plas DR, Dephoure N, Yoon SO. mTOR inhibition reprograms cellular proteostasis by regulating eIF3D-mediated selective mRNA translation and promotes cell phenotype switching. Cell Rep 2023; 42:112868. [PMID: 37494188 PMCID: PMC10528759 DOI: 10.1016/j.celrep.2023.112868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 05/31/2023] [Accepted: 07/11/2023] [Indexed: 07/28/2023] Open
Abstract
Cells maintain and dynamically change their proteomes according to the environment and their needs. Mechanistic target of rapamycin (mTOR) is a key regulator of proteostasis, homeostasis of the proteome. Thus, dysregulation of mTOR leads to changes in proteostasis and the consequent progression of diseases, including cancer. Based on the physiological and clinical importance of mTOR signaling, we investigated mTOR feedback signaling, proteostasis, and cell fate. Here, we reveal that mTOR targeting inhibits eIF4E-mediated cap-dependent translation, but feedback signaling activates a translation initiation factor, eukaryotic translation initiation factor 3D (eIF3D), to sustain alternative non-canonical translation mechanisms. Importantly, eIF3D-mediated protein synthesis enables cell phenotype switching from proliferative to more migratory. eIF3D cooperates with mRNA-binding proteins such as heterogeneous nuclear ribonucleoprotein F (hnRNPF), heterogeneous nuclear ribonucleoprotein K (hnRNPK), and Sjogren syndrome antigen B (SSB) to support selective mRNA translation following mTOR inhibition, which upregulates and activates proteins involved in insulin receptor (INSR)/insulin-like growth factor 1 receptor (IGF1R)/insulin receptor substrate (IRS) and interleukin 6 signal transducer (IL-6ST)/Janus kinase (JAK)/signal transducer and activator of transcription (STAT) signaling. Our study highlights the mechanisms by which cells establish the dynamic change of proteostasis and the resulting phenotype switch.
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Affiliation(s)
- Sejeong Shin
- Department of Physiology and Biophysics, University of Illinois College of Medicine at Chicago, Chicago, IL 60612, USA
| | - Min-Joon Han
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | | | - Ziyang Zhang
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - David R Plas
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Noah Dephoure
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10021, USA
| | - Sang-Oh Yoon
- Department of Physiology and Biophysics, University of Illinois College of Medicine at Chicago, Chicago, IL 60612, USA.
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2
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Cho S, Chun Y, He L, Ramirez CB, Ganesh KS, Jeong K, Song J, Cheong JG, Li Z, Choi J, Kim J, Koundouros N, Ding F, Dephoure N, Jang C, Blenis J, Lee G. FAM120A couples SREBP-dependent transcription and splicing of lipogenesis enzymes downstream of mTORC1. Mol Cell 2023; 83:3010-3026.e8. [PMID: 37595559 PMCID: PMC10494788 DOI: 10.1016/j.molcel.2023.07.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 05/23/2023] [Accepted: 07/15/2023] [Indexed: 08/20/2023]
Abstract
The mechanistic target of rapamycin complex 1 (mTORC1) is a master regulator of cell growth that stimulates macromolecule synthesis through transcription, RNA processing, and post-translational modification of metabolic enzymes. However, the mechanisms of how mTORC1 orchestrates multiple steps of gene expression programs remain unclear. Here, we identify family with sequence similarity 120A (FAM120A) as a transcription co-activator that couples transcription and splicing of de novo lipid synthesis enzymes downstream of mTORC1-serine/arginine-rich protein kinase 2 (SRPK2) signaling. The mTORC1-activated SRPK2 phosphorylates splicing factor serine/arginine-rich splicing factor 1 (SRSF1), enhancing its binding to FAM120A. FAM120A directly interacts with a lipogenic transcription factor SREBP1 at active promoters, thereby bridging the newly transcribed lipogenic genes from RNA polymerase II to the SRSF1 and U1-70K-containing RNA-splicing machinery. This mTORC1-regulated, multi-protein complex promotes efficient splicing and stability of lipogenic transcripts, resulting in fatty acid synthesis and cancer cell proliferation. These results elucidate FAM120A as a critical transcription co-factor that connects mTORC1-dependent gene regulation programs for anabolic cell growth.
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Affiliation(s)
- Sungyun Cho
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Yujin Chun
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Long He
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Cuauhtemoc B Ramirez
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California Irvine, Irvine, CA, USA; Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Kripa S Ganesh
- Department of Biochemistry, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Kyungjo Jeong
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, South Korea
| | - Junho Song
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, South Korea
| | - Jin Gyu Cheong
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Zhongchi Li
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Jungmin Choi
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, South Korea; Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Joohwan Kim
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Nikos Koundouros
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA; Meyer Cancer Center, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Fangyuan Ding
- Department of Biomedical Engineering, Department of Developmental and Cell Biology, Department of Pharmaceutical Sciences, Center for Synthetic Biology, and Center for Neural Circuit Mapping, University of California Irvine, Irvine, CA, USA; Center for Complex Biological Systems and Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA
| | - Noah Dephoure
- Meyer Cancer Center, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Cholsoon Jang
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA; Center for Complex Biological Systems and Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA; Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA, USA
| | - John Blenis
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA; Meyer Cancer Center, Weill Cornell Medicine, Cornell University, New York, NY, USA.
| | - Gina Lee
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California Irvine, Irvine, CA, USA; Center for Complex Biological Systems and Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA, USA; Center for Epigenetics and Metabolism, University of California Irvine, Irvine, CA, USA.
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3
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Letian A, Lemma EY, Cavaliere P, Dephoure N, Altorki NK, McGraw TE. Proximity proteome mapping reveals PD-L1-dependent pathways disrupted by anti-PD-L1 antibody specifically in EGFR-mutant lung cancer cells. Cell Commun Signal 2023; 21:58. [PMID: 36915197 PMCID: PMC10010028 DOI: 10.1186/s12964-023-01084-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/14/2023] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND PD-L1, a transmembrane ligand for immune checkpoint receptor PD1, has been successfully targeted to activate an anti-tumor immune response in a variety of solid tumors, including non-small cell lung cancer (NSCLC). Despite the success of targeting PD-L1, only about 20% of patients achieve a durable response. The reasons for the heterogeneity in response are not understood, although some molecular subtypes (e.g., mutant EGF receptor tumors) are generally poor responders. Although PD-L1 is best characterized as a transmembrane PD1 ligand, the emerging view is that PD-L1 has functions independent of activating PD1 signaling. It is not known whether these cell-intrinsic functions of PD-L1 are shared among non-transformed and transformed cells, if they vary among cancer molecular subtypes, or if they are impacted by anti-PD-L1 therapy. METHODS Here we use quantitative microscopy techniques and APEX2 proximity mapping to describe the behavior of PD-L1 and to identify PD-L1's proximal proteome in human lung epithelial cells. RESULTS Our data reveal growth factor control of PD-L1 recycling as a mechanism for acute and reversible regulation of PD-L1 density on the plasma membrane. In addition, we describe novel PD-L1 biology restricted to mutant EGFR cells. Anti-PD-L1 antibody treatment of mutant EGFR cells perturbs cell intrinsic PD-L1 functions, leading to reduced cell migration, increased half-life of EGFR and increased extracellular vesicle biogenesis, whereas anti-PD-L1 antibody does not induce these changes in wild type EGFR cells. CONCLUSIONS Growth factor acute regulation of PD-L1 trafficking, by contributing to the control of plasma membrane density, might contribute to the regulation of PD-L1's immune checkpoint activity, whereas the specific effects of anti-PD-L1 on mutant EGFR cells might contribute to the poor anti-PD-L1 response of mutant EGFR tumors. Video Abstract.
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Affiliation(s)
- Anudari Letian
- Department of Biochemistry, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065 USA
- Biochemistry, Cell and Molecular Biology Graduate Program, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065 USA
| | - Eyoel Yemanaberhan Lemma
- Department of Biochemistry, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065 USA
- Department of Cardiothoracic Surgery, Weill Cornell Medicine and NY Presbyterian Hospital, 1300 York Ave, New York, NY 10065 USA
| | - Paola Cavaliere
- Department of Biochemistry, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065 USA
| | - Noah Dephoure
- Department of Biochemistry, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065 USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine and NY Presbyterian Hospital, 1300 York Ave, New York, NY 10065 USA
| | - Nasser K. Altorki
- Department of Cardiothoracic Surgery, Weill Cornell Medicine and NY Presbyterian Hospital, 1300 York Ave, New York, NY 10065 USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine and NY Presbyterian Hospital, 1300 York Ave, New York, NY 10065 USA
- Neuberger Berman Foundation Lung Cancer Research Center, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065 USA
| | - Timothy E. McGraw
- Department of Biochemistry, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065 USA
- Department of Cardiothoracic Surgery, Weill Cornell Medicine and NY Presbyterian Hospital, 1300 York Ave, New York, NY 10065 USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine and NY Presbyterian Hospital, 1300 York Ave, New York, NY 10065 USA
- Neuberger Berman Foundation Lung Cancer Research Center, Weill Cornell Medicine, 1300 York Ave, New York, NY 10065 USA
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4
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Li Z, Low V, Luga V, Sun J, Earlie E, Parang B, Shobana Ganesh K, Cho S, Endress J, Schild T, Hu M, Lyden D, Jin W, Guo C, Dephoure N, Cantley LC, Laughney AM, Blenis J. Tumor-produced and aging-associated oncometabolite methylmalonic acid promotes cancer-associated fibroblast activation to drive metastatic progression. Nat Commun 2022; 13:6239. [PMID: 36266345 PMCID: PMC9584945 DOI: 10.1038/s41467-022-33862-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 10/05/2022] [Indexed: 12/25/2022] Open
Abstract
The systemic metabolic shifts that occur during aging and the local metabolic alterations of a tumor, its stroma and their communication cooperate to establish a unique tumor microenvironment (TME) fostering cancer progression. Here, we show that methylmalonic acid (MMA), an aging-increased oncometabolite also produced by aggressive cancer cells, activates fibroblasts in the TME, which reciprocally secrete IL-6 loaded extracellular vesicles (EVs) that drive cancer progression, drug resistance and metastasis. The cancer-associated fibroblast (CAF)-released EV cargo is modified as a result of reactive oxygen species (ROS) generation and activation of the canonical and noncanonical TGFβ signaling pathways. EV-associated IL-6 functions as a stroma-tumor messenger, activating the JAK/STAT3 and TGFβ signaling pathways in tumor cells and promoting pro-aggressive behaviors. Our findings define the role of MMA in CAF activation to drive metastatic reprogramming, unveiling potential therapeutic avenues to target MMA at the nexus of aging, the tumor microenvironment and metastasis.
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Affiliation(s)
- Zhongchi Li
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10021, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Vivien Low
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10021, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Valbona Luga
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10021, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Janet Sun
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10021, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Ethan Earlie
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10021, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Bobak Parang
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10021, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, 10021, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Kripa Shobana Ganesh
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10021, USA
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Sungyun Cho
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10021, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Jennifer Endress
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10021, USA
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Tanya Schild
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10021, USA
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, 10021, USA
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Mengying Hu
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10021, USA
- Departments of Pediatrics, and Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, 10021, USA
| | - David Lyden
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10021, USA
- Departments of Pediatrics, and Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Wenbing Jin
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Chunjun Guo
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Noah Dephoure
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10021, USA
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10021, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
- Dana Farber Cancer Institute, Boston, MA, 02215, USA
| | - Ashley M Laughney
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10021, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10021, USA
| | - John Blenis
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10021, USA.
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, 10021, USA.
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, 10021, USA.
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5
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Low V, Li Z, Laughney A, Jin W, Dephoure N, Luga V, Earlie E, Parang B, Guo C, Cantley L, Blenis J. Abstract 3175: Methylmalonic acid in TME signaling. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The importance of metabolic reprogramming in cancer has been long demonstrated by the association of systemic metabolic changes, such as aging, diet and exercise, with cancer outcomes. These systemic shifts, combined with local metabolic alterations within the tumor microenvironment (TME), can all cooperate to foster an environment conducive to cancer progression. In cells derived from primary and metastatic patient tumors, we found that mesenchymal-like cells displayed dysregulated propionate metabolism, leading to increased accumulation and secretion of methylmalonic acid (MMA), a novel aging-induced oncometabolite. This tumor cell-secreted MMA, in addition to increased MMA in the serum of elderly individuals, combine to form high local accumulation of MMA in the TME. We discovered that MMA acts on fibroblasts in the TME, activating them to cancer-associated fibroblasts (CAFs). MMA modifies the cargo of CAF-secreted extracellular vesicles (EVs), which function as a messenger to tumor cells, further promoting epithelial-to-mesenchymal transition, drug resistance, and increased metastasis in vivo. Here, we reveal a novel function of MMA in cancer, demonstrating for the first time that tumor-secreted MMA recruits the tumor microenvironment to drive cancer progression and metastatic reprogramming.
Citation Format: Vivien Low, Zhongchi Li, Ashley Laughney, Wenbing Jin, Noah Dephoure, Valbona Luga, Ethan Earlie, Bobak Parang, Chunjun Guo, Lewis Cantley, John Blenis. Methylmalonic acid in TME signaling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3175.
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Ganesh KS, Schaffer B, Lee G, Johnson J, Yaron TM, Dephoure N, Cantley LC, Blenis J. Abstract 162: Identification of novel targets of Serine/arginine-rich protein-specific kinase 2. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Altered metabolism is one of the hallmarks of cancer cells, supporting aberrant proliferation and survival in nutrient scarce and stressful environments. The reprogrammed metabolism supports the acquisition of malignant traits, increasing cellular fitness and providing a selective advantage in tumorigenesis. Multiple signaling cascades converge to regulate cancer cell metabolism to maintain a delicate balance between anabolic and catabolic processes, with the overall goal to fuel ATP production, biosynthesis of macromolecules and maintaining redox balance. Specifically, 70% of human cancers have hyperactivated mechanistic target of rapamycin (mTOR) signaling, the master regulator of cellular metabolism. As an important signaling node, mTOR complex 1(mTORC1) integrates upstream stimuli such as growth factors, amino acids and oxygen levels to regulate a myriad of anabolic processes including protein and nucleotide synthesis, RNA biogenesis and lipid metabolism, thereby promoting cell growth. The highly proliferative state of cancer cells, coupled with a change in energy demands, forces these cells to rewire their cellular metabolism to increase production of cellular building blocks like proteins, lipids and nucleotides. De novo lipogenesis provides lipids which act as an integral component of the plasma membrane as well as functioning as signaling molecules. In addition to promoting various anabolic processes, our lab has demonstrated that mTORC1-activated serine/arginine-rich protein-specific kinase 2 (SRPK2) phosphorylates splicing factors that stabilize lipogenic transcripts, protecting them from nonsense-mediated decay and thereby increasing de novo lipogenesis. This is in contrast to another serine/arginine-rich protein-specific kinase 1 (SRPK1), which is not regulated by mTORC1. Inhibition of the mTORC1-SRPK2 signaling axis blunts de novo lipogenesis and impedes tumor growth in several tumor xenograft models. SRPK2 overexpression is also observed in lung and colon cancers, suggesting SRPK2 may promote the growth of some human tumors. Despite the emerging role for SRPK2 in tumor growth, very few substrates of this kinase are known. We conducted a phospho-proteomics screen to identify novel substrates of SRPK1 and SRPK2. While some of the targets we identified are regulated in an mTORC1-dependent manner, many appear to be regulated independent of mTORC1, such as PTP1B, EGLN1 and EI24. We hypothesize that these mTORC1-independent targets could be SRPK1-dependent revealing potential distinct branches of SRPK signaling. Future studies will focus on not only validating a subset of these novel targets and their role in tumor growth, but also on exploring mTORC1-dependent and independent SRPK signaling.
Citation Format: Kripa Shobana Ganesh, Bethany Schaffer, Gina Lee, Jared Johnson, Tomer M. Yaron, Noah Dephoure, Lewis C. Cantley, John Blenis. Identification of novel targets of Serine/arginine-rich protein-specific kinase 2 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 162.
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Affiliation(s)
| | | | - Gina Lee
- 2UC Irvine School of Medicine, Irvine, CA
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7
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Raman R, Villefranc JA, Ullmann TM, Thiesmeyer J, Anelli V, Yao J, Hurley JR, Pauli C, Bareja R, Wha Eng K, Dorsaint P, Wilkes DC, Beg S, Kudman S, Shaw R, Churchill M, Ahmed A, Keefer L, Misner I, Nichol D, Gumpeni N, Scognamiglio T, Rubin MA, Grandori C, Solomon JP, Song W, Mosquera JM, Dephoure N, Sboner A, Elemento O, Houvras Y. Inhibition of FGF receptor blocks adaptive resistance to RET inhibition in CCDC6-RET-rearranged thyroid cancer. J Exp Med 2022; 219:e20210390. [PMID: 35510953 PMCID: PMC9082625 DOI: 10.1084/jem.20210390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 11/23/2021] [Accepted: 03/18/2022] [Indexed: 11/18/2022] Open
Abstract
Genetic alterations in RET lead to activation of ERK and AKT signaling and are associated with hereditary and sporadic thyroid cancer and lung cancer. Highly selective RET inhibitors have recently entered clinical use after demonstrating efficacy in treating patients with diverse tumor types harboring RET gene rearrangements or activating mutations. In order to understand resistance mechanisms arising after treatment with RET inhibitors, we performed a comprehensive molecular and genomic analysis of a patient with RET-rearranged thyroid cancer. Using a combination of drug screening and proteomic and biochemical profiling, we identified an adaptive resistance to RET inhibitors that reactivates ERK signaling within hours of drug exposure. We found that activation of FGFR signaling is a mechanism of adaptive resistance to RET inhibitors that activates ERK signaling. Combined inhibition of FGFR and RET prevented the development of adaptive resistance to RET inhibitors, reduced cell viability, and decreased tumor growth in cellular and animal models of CCDC6-RET-rearranged thyroid cancer.
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Affiliation(s)
- Renuka Raman
- Department of Surgery, Weill Cornell Medical College, New York, NY
| | | | | | | | - Viviana Anelli
- Department of Surgery, Weill Cornell Medical College, New York, NY
| | - Jun Yao
- Department of Surgery, Weill Cornell Medical College, New York, NY
| | - James R. Hurley
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Chantal Pauli
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Rohan Bareja
- The Caryl and Israel Englander Institute for Precision Medicine and the Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY
| | - Kenneth Wha Eng
- The Caryl and Israel Englander Institute for Precision Medicine and the Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY
| | - Princesca Dorsaint
- The Caryl and Israel Englander Institute for Precision Medicine and the Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY
| | - David C. Wilkes
- The Caryl and Israel Englander Institute for Precision Medicine and the Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY
| | - Shaham Beg
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Sarah Kudman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Reid Shaw
- SEngine Precision Medicine, Seattle, WA
| | | | - Adnan Ahmed
- Department of Biochemistry, Weill Cornell Medical College, New York, NY
| | | | - Ian Misner
- Personal Genome Diagnostics, Inc., Baltimore, MD
| | - Donna Nichol
- Personal Genome Diagnostics, Inc., Baltimore, MD
| | - Naveen Gumpeni
- Department of Radiology, Weill Cornell Medical College, New York, NY
| | - Theresa Scognamiglio
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Mark A. Rubin
- Bern Center for Precision Medicine, University of Bern, Bern, Switzerland
| | | | - James Patrick Solomon
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Wei Song
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Juan Miguel Mosquera
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Noah Dephoure
- Department of Biochemistry, Weill Cornell Medical College, New York, NY
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medical College, New York, NY
| | - Andrea Sboner
- The Caryl and Israel Englander Institute for Precision Medicine and the Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medical College, New York, NY
| | - Olivier Elemento
- The Caryl and Israel Englander Institute for Precision Medicine and the Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medical College, New York, NY
| | - Yariv Houvras
- Department of Surgery, Weill Cornell Medical College, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medical College, New York, NY
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8
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Ramchandani D, Berisa M, Tavarez DA, Li Z, Miele M, Bai Y, Lee SB, Ban Y, Dephoure N, Hendrickson RC, Cloonan SM, Gao D, Cross JR, Vahdat LT, Mittal V. Copper depletion modulates mitochondrial oxidative phosphorylation to impair triple negative breast cancer metastasis. Nat Commun 2021; 12:7311. [PMID: 34911956 PMCID: PMC8674260 DOI: 10.1038/s41467-021-27559-z] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 11/05/2021] [Indexed: 12/26/2022] Open
Abstract
Copper serves as a co-factor for a host of metalloenzymes that contribute to malignant progression. The orally bioavailable copper chelating agent tetrathiomolybdate (TM) has been associated with a significant survival benefit in high-risk triple negative breast cancer (TNBC) patients. Despite these promising data, the mechanisms by which copper depletion impacts metastasis are poorly understood and this remains a major barrier to advancing TM to a randomized phase II trial. Here, using two independent TNBC models, we report a discrete subpopulation of highly metastatic SOX2/OCT4+ cells within primary tumors that exhibit elevated intracellular copper levels and a marked sensitivity to TM. Global proteomic and metabolomic profiling identifies TM-mediated inactivation of Complex IV as the primary metabolic defect in the SOX2/OCT4+ cell population. We also identify AMPK/mTORC1 energy sensor as an important downstream pathway and show that AMPK inhibition rescues TM-mediated loss of invasion. Furthermore, loss of the mitochondria-specific copper chaperone, COX17, restricts copper deficiency to mitochondria and phenocopies TM-mediated alterations. These findings identify a copper-metabolism-metastasis axis with potential to enrich patient populations in next-generation therapeutic trials.
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Affiliation(s)
- Divya Ramchandani
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Mirela Berisa
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Diamile A Tavarez
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Zhuoning Li
- Department of Microchemistry and Proteomics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Matthew Miele
- Department of Microchemistry and Proteomics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yang Bai
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Sharrell B Lee
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Yi Ban
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Noah Dephoure
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Ronald C Hendrickson
- Department of Microchemistry and Proteomics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Suzanne M Cloonan
- Department of Pulmonary and Critical Care Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
- The School of Medicine and Tallaght University Hospital, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Dingcheng Gao
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York, NY, 10065, USA
- Department of Cell and Developmental biology, Weill Cornell Medicine, New York, NY, 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Justin R Cross
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Linda T Vahdat
- Department of Medicine, Breast Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
| | - Vivek Mittal
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York, NY, 10065, USA.
- Department of Cell and Developmental biology, Weill Cornell Medicine, New York, NY, 10065, USA.
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA.
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9
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Egan CE, Stefanova D, Ahmed A, Raja VJ, Thiesmeyer JW, Chen KJ, Greenberg JA, Zhang T, He B, Finnerty BM, Zarnegar R, Jin MM, Scognamiglio T, Dephoure N, Fahey T, Min IM. CSPG4 Is a Potential Therapeutic Target in Anaplastic Thyroid Cancer. Thyroid 2021; 31:1481-1493. [PMID: 34078123 PMCID: PMC8917884 DOI: 10.1089/thy.2021.0067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Background: Anaplastic thyroid cancer (ATC) is a rare cancer with poor prognosis and few treatment options. The objective of this study was to investigate new immune-associated therapeutic targets by identifying ATC-derived, human leukocyte antigen (HLA) class II-presenting peptides. One protein that generated multiple peptides in ATC was chondroitin sulfate-proteoglycan-4 (CSPG4), a transmembrane proteoglycan with increased expression in multiple aggressive cancers, but not yet investigated in ATC. Methods: We applied autologous peripheral blood T cells to ATC patient-derived xenografted mice to examine whether ATC induces a tumor-specific T cell response. We then identified peptide antigens eluted from the HLA-DQ complex in ATC patient-derived cells using mass spectrometry, detecting abundant CSPG4-derived peptides specific to the ATC sample. Next, we analyzed the surface expression level of CSPG4 in thyroid cancer cell lines and primary cell culture using flow cytometry. In addition, we used immunohistochemistry to compare the expression level and localization of the CSPG4 protein in ATC, papillary thyroid cancer, and normal thyroid tissue. We then investigated the correlation between CSPG4 expression and clinicopathological features of patients with thyroid cancer. Results: We found that ATC tissue had a high level of HLA-DQ expression and that the patient's CD4+ T cells showed activation when exposed to ATC. By eluting the HLA-DQ complex of ATC tissue, we found that CSPG4 generated one of the most abundant and specific peptides. CSPG4 expression at the cell surface of thyroid cancer was also significantly high when determined by flow cytometry, with the majority of ATC cell lines exhibiting ∼10-fold higher mean fluorescence intensity. Furthermore, most ATC patient cases expressed CSPG4 in the cytoplasm or membrane of the tumor cells. CSPG4 expression was correlated with tumor size, extrathyroidal extension, and intercellular adhesion molecule-1 (ICAM-1) circumferential expression. CSPG4 mRNA overexpression was associated with worse overall survival in patients with ATC and poorly differentiated thyroid cancer. Conclusions: CSPG4 expression is significantly elevated in aggressive thyroid cancers, with a strong correlation with a poor prognosis. The vast number of HLA-DQ eluted CSPG4 peptides was identified in ATC, demonstrating the potential of CSPG4 as a novel immunotherapeutic target for ATC.
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Affiliation(s)
- Caitlin E. Egan
- Department of Surgery, Weill Cornell Medicine, New York, New York, USA
| | | | - Adnan Ahmed
- Department of Biochemistry, Weill Cornell Medicine, New York, New York, USA
| | - Vijay J. Raja
- Department of Biochemistry, Weill Cornell Medicine, New York, New York, USA
| | | | - Kevin J. Chen
- Department of Surgery, Weill Cornell Medicine, New York, New York, USA
| | | | - Taotao Zhang
- Department of Pathology, and Weill Cornell Medicine, New York, New York, USA
| | - Bing He
- Department of Pathology, and Weill Cornell Medicine, New York, New York, USA
| | | | - Rasa Zarnegar
- Department of Surgery, Weill Cornell Medicine, New York, New York, USA
| | - Moonsoo M. Jin
- Department of Surgery, Weill Cornell Medicine, New York, New York, USA
- Department of Radiology, Weill Cornell Medicine, New York, New York, USA
| | | | - Noah Dephoure
- Department of Biochemistry, Weill Cornell Medicine, New York, New York, USA
- Address correspondence to: Noah Dephoure, PhD, Weill Cornell Medicine, Department of Biochemistry, 1300 York Avenue, New York, NY 10065, USA
| | - Thomas Fahey
- Department of Surgery, Weill Cornell Medicine, New York, New York, USA
- Thomas Fahey III, MD, Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Irene M. Min
- Department of Surgery, Weill Cornell Medicine, New York, New York, USA
- Irene M. Min, PhD, Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
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10
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Raman R, Villefranc J, Ullmann T, Thiesmeyer J, Anelli V, Pauli C, Bareja R, Eng KW, Dorsaint P, Wilkes D, Beg S, Shaw R, Churchill M, Gumpeni N, Scognamiglio T, Rubin M, Grandori C, Mosquera J, Mosquera J, Mosquera J, Dephoure N, Sboner A, Elemento O, Houvras Y. Abstract 1434: Uncovering the mechanism of adaptive resistance to RET inhibitors in RET rearranged thyroid cancer. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-1434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Kinase inhibitors are a critical tool for cancer treatment, but their efficacy is limited by resistance mechanisms. In thyroid and lung cancer RET gene rearrangements result in constitutive MAPK pathway activation and drive malignancy. While treatment with new selective RET inhibitors has been associated with significant clinical responses, a majority of patients experience a partial response or disease stabilization as their best clinical outcome. Resistance to RET inhibitors has emerged as a clinical problem requiring new treatment strategies. Using a combination of drug screening, proteomic, and biochemical profiling we identified a strategy to overcome adaptive resistance to RET inhibitors in human thyroid cancer cell lines and vertebrate animal models. The identification of alternative signaling pathways that reactivates ERK signaling as a mechanism of resistance to RET inhibitors provides an opportunity to anticipate resistance to selective RET inhibitors and use combination therapy that leads to more significant and durable anti-tumor responses in patients with RET rearranged cancers.
Citation Format: Renuka Raman, Jacques Villefranc, Timothy Ullmann, Jessica Thiesmeyer, Viviana Anelli, Chantal Pauli, Rohan Bareja, Kenneth Wha Eng, Princesca Dorsaint, David Wilkes, Shaham Beg, Reid Shaw, Michael Churchill, Naveen Gumpeni, Theresa Scognamiglio, Mark Rubin, Carla Grandori, Juan Mosquera, Juan Mosquera, Juan Mosquera, Noah Dephoure, Andrea Sboner, Olivier Elemento, Yariv Houvras. Uncovering the mechanism of adaptive resistance to RET inhibitors in RET rearranged thyroid cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1434.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Shaham Beg
- 1Weill Cornell Medical College, New York, NY
| | - Reid Shaw
- 3SEngine Precision Medicine, Seattle, WA
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11
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Schild T, McReynolds MR, Shea C, Low V, Schaffer BE, Asara JM, Piskounova E, Dephoure N, Rabinowitz JD, Gomes AP, Blenis J. NADK is activated by oncogenic signaling to sustain pancreatic ductal adenocarcinoma. Cell Rep 2021; 35:109238. [PMID: 34133937 DOI: 10.1016/j.celrep.2021.109238] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 04/02/2021] [Accepted: 05/18/2021] [Indexed: 12/28/2022] Open
Abstract
Metabolic adaptations and the signaling events that control them promote the survival of pancreatic ductal adenocarcinoma (PDAC) at the fibrotic tumor site, overcoming stresses associated with nutrient and oxygen deprivation. Recently, rewiring of NADPH production has been shown to play a key role in this process. NADPH is recycled through reduction of NADP+ by several enzymatic systems in cells. However, de novo NADP+ is synthesized only through one known enzymatic reaction, catalyzed by NAD+ kinase (NADK). In this study, we show that oncogenic KRAS promotes protein kinase C (PKC)-mediated NADK phosphorylation, leading to its hyperactivation, thus sustaining both NADP+ and NADPH levels in PDAC cells. Together, our data show that increased NADK activity is an important adaptation driven by oncogenic signaling. Our findings indicate that NADK could serve as a much-needed therapeutic target for PDAC.
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Affiliation(s)
- Tanya Schild
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA; Department of Biochemistry, Weill Cornell Medicine, New York, NY 10021, USA
| | | | - Christie Shea
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA; Tri-institutional PhD Program in Chemical Biology, New York, NY 10021, USA
| | - Vivien Low
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA; Department of Biochemistry, Weill Cornell Medicine, New York, NY 10021, USA
| | - Bethany E Schaffer
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA
| | - John M Asara
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Elena Piskounova
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Biochemistry, Weill Cornell Medicine, New York, NY 10021, USA; Department of Dermatology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Noah Dephoure
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10021, USA
| | | | - Ana P Gomes
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA.
| | - John Blenis
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA.
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12
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Lhuillier C, Rudqvist NP, Yamazaki T, Zhang T, Charpentier M, Galluzzi L, Dephoure N, Clement CC, Santambrogio L, Zhou XK, Formenti SC, Demaria S. Radiotherapy-exposed CD8+ and CD4+ neoantigens enhance tumor control. J Clin Invest 2021; 131:138740. [PMID: 33476307 DOI: 10.1172/jci138740] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 01/13/2021] [Indexed: 12/23/2022] Open
Abstract
Neoantigens generated by somatic nonsynonymous mutations are key targets of tumor-specific T cells, but only a small number of mutations predicted to be immunogenic are presented by MHC molecules on cancer cells. Vaccination studies in mice and patients have shown that the majority of neoepitopes that elicit T cell responses fail to induce significant antitumor activity, for incompletely understood reasons. We report that radiotherapy upregulates the expression of genes containing immunogenic mutations in a poorly immunogenic mouse model of triple-negative breast cancer. Vaccination with neoepitopes encoded by these genes elicited CD8+ and CD4+ T cells that, whereas ineffective in preventing tumor growth, improved the therapeutic efficacy of radiotherapy. Mechanistically, neoantigen-specific CD8+ T cells preferentially killed irradiated tumor cells. Neoantigen-specific CD4+ T cells were required for the therapeutic efficacy of vaccination and acted by producing Th1 cytokines, killing irradiated tumor cells, and promoting epitope spread. Such a cytotoxic activity relied on the ability of radiation to upregulate class II MHC molecules as well as the death receptors FAS/CD95 and DR5 on the surface of tumor cells. These results provide proof-of-principle evidence that radiotherapy works in concert with neoantigen vaccination to improve tumor control.
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Affiliation(s)
| | | | | | - Tuo Zhang
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York, USA
| | | | - Lorenzo Galluzzi
- Department of Radiation Oncology and.,Sandra and Edward Meyer Cancer Center, New York, New York, USA.,Caryl and Israel Englander Institute for Precision Medicine, New York, New York, USA
| | - Noah Dephoure
- Sandra and Edward Meyer Cancer Center, New York, New York, USA.,Department of Biochemistry
| | | | - Laura Santambrogio
- Department of Radiation Oncology and.,Caryl and Israel Englander Institute for Precision Medicine, New York, New York, USA
| | - Xi Kathy Zhou
- Division of Biostatistics and Epidemiology, Department of Healthcare Policy and Research, and
| | - Silvia C Formenti
- Department of Radiation Oncology and.,Sandra and Edward Meyer Cancer Center, New York, New York, USA.,Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Sandra Demaria
- Department of Radiation Oncology and.,Sandra and Edward Meyer Cancer Center, New York, New York, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
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13
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Cyrta J, Augspach A, De Filippo MR, Prandi D, Thienger P, Benelli M, Cooley V, Bareja R, Wilkes D, Chae SS, Cavaliere P, Dephoure N, Uldry AC, Lagache SB, Roma L, Cohen S, Jaquet M, Brandt LP, Alshalalfa M, Puca L, Sboner A, Feng F, Wang S, Beltran H, Lotan T, Spahn M, Kruithof-de Julio M, Chen Y, Ballman KV, Demichelis F, Piscuoglio S, Rubin MA. Role of specialized composition of SWI/SNF complexes in prostate cancer lineage plasticity. Nat Commun 2020; 11:5549. [PMID: 33144576 PMCID: PMC7642293 DOI: 10.1038/s41467-020-19328-1] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 10/07/2020] [Indexed: 01/06/2023] Open
Abstract
Advanced prostate cancer initially responds to hormonal treatment, but ultimately becomes resistant and requires more potent therapies. One mechanism of resistance observed in around 10–20% of these patients is lineage plasticity, which manifests in a partial or complete small cell or neuroendocrine prostate cancer (NEPC) phenotype. Here, we investigate the role of the mammalian SWI/SNF (mSWI/SNF) chromatin remodeling complex in NEPC. Using large patient datasets, patient-derived organoids and cancer cell lines, we identify mSWI/SNF subunits that are deregulated in NEPC and demonstrate that SMARCA4 (BRG1) overexpression is associated with aggressive disease. We also show that SWI/SNF complexes interact with different lineage-specific factors in NEPC compared to prostate adenocarcinoma. These data point to a role for mSWI/SNF complexes in therapy-related lineage plasticity, which may also be relevant for other solid tumors. The differentiation of prostate adenocarcinoma to neuroendocrine prostate cancer (CRPC-NE) is a mechanism of resistance to androgen deprivation therapy. Here the authors show that SWI/SNF chromatin-remodeling complex is deregulated in CRPC-NE and that the complex interacts with different lineage specific factors throughout prostate cancer transdifferentiation.
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Affiliation(s)
- Joanna Cyrta
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland.,The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Anke Augspach
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Maria Rosaria De Filippo
- Department for BioMedical Research, Urology Research Laboratory, University of Bern, 3008, Bern, Switzerland.,Institute of Pathology and Medical Genetics, University Hospital Basel, University of Basel, 4051, Basel, Switzerland
| | - Davide Prandi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38122, Trento, Italy
| | - Phillip Thienger
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Matteo Benelli
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38122, Trento, Italy.,Bioinformatics Unit, Hospital of Prato, 59100, Prato, Italy
| | - Victoria Cooley
- Department of Healthcare Policy and Research, Division of Biostatistics and Epidemiology, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Rohan Bareja
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, 10021, USA.,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - David Wilkes
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Sung-Suk Chae
- Department of Laboratory Medicine and Pathology, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Paola Cavaliere
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Noah Dephoure
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10021, USA.,Department of Biochemistry, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Anne-Christine Uldry
- Proteomics Mass Spectrometry Core Facility, University of Bern, 3010, Bern, Switzerland
| | - Sophie Braga Lagache
- Proteomics Mass Spectrometry Core Facility, University of Bern, 3010, Bern, Switzerland
| | - Luca Roma
- Institute of Pathology and Medical Genetics, University Hospital Basel, University of Basel, 4051, Basel, Switzerland
| | - Sandra Cohen
- Department of Laboratory Medicine and Pathology, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Muriel Jaquet
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Laura P Brandt
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Mohammed Alshalalfa
- Department of Radiation Oncology, Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
| | - Loredana Puca
- Department of Medicine, Division of Medical Oncology, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Andrea Sboner
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, 10021, USA.,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021, USA.,HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021, USA.,Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Felix Feng
- Proteomics Mass Spectrometry Core Facility, University of Bern, 3010, Bern, Switzerland
| | - Shangqian Wang
- Human Oncology and Pathogenesis Program and Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Himisha Beltran
- Department of Medicine, Division of Medical Oncology, Weill Cornell Medicine, New York, NY, 10021, USA.,Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Tamara Lotan
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Martin Spahn
- Lindenhofspital Bern, Prostate Center Bern, 3012, Bern, Switzerland.,Department of Urology, Essen University Hospital, University of Duisburg-Essen, 47057, Essen, Germany
| | - Marianna Kruithof-de Julio
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland.,Department for BioMedical Research, Urology Research Laboratory, University of Bern, 3008, Bern, Switzerland.,Department of Urology, Inselspital, 3010, Bern, Switzerland
| | - Yu Chen
- Department of Medicine, Division of Medical Oncology, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Karla V Ballman
- Department of Healthcare Policy and Research, Division of Biostatistics and Epidemiology, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Francesca Demichelis
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, 10021, USA.,Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38122, Trento, Italy
| | - Salvatore Piscuoglio
- Institute of Pathology and Medical Genetics, University Hospital Basel, University of Basel, 4051, Basel, Switzerland.,Visceral Surgery Research Laboratory, Clarunis, Department of Biomedicine, University of Basel, 4051, Basel, Switzerland.,Clarunis Universitäres Bauchzentrum Basel, 4002, Basel, Switzerland
| | - Mark A Rubin
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland. .,Inselspital, 3010, Bern, Switzerland. .,Bern Center for Precision Medicine, 3008, Bern, Switzerland.
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14
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Blenis J, Lee G, Cho S, Zheng Y, Jang C, Cantley L, Rabinowitz J, Dephoure N. Abstract IA12: Coordination of mRNA processing, translation, and metabolism by mTORC1. Mol Cancer Res 2020. [DOI: 10.1158/1557-3125.pi3k-mtor18-ia12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The mTOR complex 1 (mTORC1)–S6 protein kinase (S6K1) signaling pathway has evolved to sense and respond to changes in growth factor and hormone-dependent signaling, cellular energy status, nutrient availability, and surrounding oxygen concentrations. A major mechanism through which mTOR regulates downstream processes is via the coordinated regulation of gene expression, mRNA biogenesis, protein synthesis, and protein degradation. I will discuss our studies linking mTORC1/S6K1 to mRNA processing, metabolism, and cancer progression.
Citation Format: John Blenis, Gina Lee, Sungyun Cho, Yuxiang Zheng, Cholsoon Jang, Lew Cantley, Joshua Rabinowitz, Noah Dephoure. Coordination of mRNA processing, translation, and metabolism by mTORC1 [abstract]. In: Proceedings of the AACR Special Conference on Targeting PI3K/mTOR Signaling; 2018 Nov 30-Dec 8; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(10_Suppl):Abstract nr IA12.
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Affiliation(s)
| | - Gina Lee
- 1Weill Cornell Medicine, New York, NY,
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15
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Gomes AP, Ilter D, Low V, Endress JE, Fernández-García J, Rosenzweig A, Schild T, Broekaert D, Ahmed A, Planque M, Elia I, Han J, Kinzig C, Mullarky E, Mutvei AP, Asara J, de Cabo R, Cantley LC, Dephoure N, Fendt SM, Blenis J. Age-induced accumulation of methylmalonic acid promotes tumour progression. Nature 2020; 585:283-287. [PMID: 32814897 PMCID: PMC7785256 DOI: 10.1038/s41586-020-2630-0] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/10/2020] [Indexed: 12/21/2022]
Abstract
From age 65 onwards, the risk of cancer incidence and associated mortality is substantially higher1–6. Nonetheless, our understanding of the complex relationship between age and cancer is still in its infancy2,3,7,8. For decades, this link has largely been attributed to increased exposure time to mutagens in older individuals. However, this view does not account for the well-established role of diet, exercise and small molecules that target the pace of metabolic aging9–12. Here, we show that metabolic alterations that occur with age can render a systemic environment favorable to progression and aggressiveness of tumors. Specifically, we show that methylmalonic acid (MMA), a by-product of propionate metabolism, is significantly up-regulated in the serum of older people, and functions as a mediator of tumor progression. We traced this to MMA’s ability to induce SOX4 and consequently eliciting a transcriptional reprogramming that can endow cancer cells with aggressive properties. Thus, accumulation of MMA represents a novel link between aging and cancer progression, implicating MMA as a novel therapeutic target for advanced carcinomas.
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Affiliation(s)
- Ana P Gomes
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA. .,Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA. .,Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA.
| | - Didem Ilter
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.,Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA.,Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Vivien Low
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.,The Biochemistry, Structural, Developmental, Cell and Molecular Biology Allied PhD Program, Weill Cornell Medicine, New York, NY, USA
| | - Jennifer E Endress
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.,The Biochemistry, Structural, Developmental, Cell and Molecular Biology Allied PhD Program, Weill Cornell Medicine, New York, NY, USA
| | - Juan Fernández-García
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium.,Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Adam Rosenzweig
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.,Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Tanya Schild
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.,The Biochemistry, Structural, Developmental, Cell and Molecular Biology Allied PhD Program, Weill Cornell Medicine, New York, NY, USA
| | - Dorien Broekaert
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium.,Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Adnan Ahmed
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.,Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - Melanie Planque
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium.,Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Ilaria Elia
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium.,Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Julie Han
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.,Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Charles Kinzig
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.,Weill Cornell Medicine/Rockefeller University/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Edouard Mullarky
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.,Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Anders P Mutvei
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.,Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - John Asara
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Rafael de Cabo
- Laboratory of Experimental Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.,Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Noah Dephoure
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.,Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - Sarah-Maria Fendt
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium.,Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Leuven, Belgium
| | - John Blenis
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA. .,Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA. .,Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA.
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16
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Gomes AP, Ilter D, Low V, Rosenzweig A, Shen ZJ, Schild T, Rivas MA, Er EE, McNally DR, Mutvei AP, Han J, Ou YH, Cavaliere P, Mullarky E, Nagiec M, Shin S, Yoon SO, Dephoure N, Massagué J, Melnick AM, Cantley LC, Tyler JK, Blenis J. Dynamic Incorporation of Histone H3 Variants into Chromatin Is Essential for Acquisition of Aggressive Traits and Metastatic Colonization. Cancer Cell 2019; 36:402-417.e13. [PMID: 31564638 PMCID: PMC6801101 DOI: 10.1016/j.ccell.2019.08.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 06/07/2019] [Accepted: 08/16/2019] [Indexed: 12/19/2022]
Abstract
Metastasis is the leading cause of cancer mortality. Chromatin remodeling provides the foundation for the cellular reprogramming necessary to drive metastasis. However, little is known about the nature of this remodeling and its regulation. Here, we show that metastasis-inducing pathways regulate histone chaperones to reduce canonical histone incorporation into chromatin, triggering deposition of H3.3 variant at the promoters of poor-prognosis genes and metastasis-inducing transcription factors. This specific incorporation of H3.3 into chromatin is both necessary and sufficient for the induction of aggressive traits that allow for metastasis formation. Together, our data clearly show incorporation of histone variant H3.3 into chromatin as a major regulator of cell fate during tumorigenesis, and histone chaperones as valuable therapeutic targets for invasive carcinomas.
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Affiliation(s)
- Ana P Gomes
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA.
| | - Didem Ilter
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Vivien Low
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Adam Rosenzweig
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Zih-Jie Shen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Tanya Schild
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Martin A Rivas
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Ekrem E Er
- Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Dylan R McNally
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Anders P Mutvei
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Julie Han
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Yi-Hung Ou
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Paola Cavaliere
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Biochemistry, Weill Cornell Medicine, New York, NY 10021, USA
| | - Edouard Mullarky
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Michal Nagiec
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Sejeong Shin
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Sang-Oh Yoon
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Noah Dephoure
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Biochemistry, Weill Cornell Medicine, New York, NY 10021, USA
| | - Joan Massagué
- Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Ari M Melnick
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Jessica K Tyler
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - John Blenis
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021, USA.
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17
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Di Giammartino DC, Kloetgen A, Polyzos A, Liu Y, Kim D, Murphy D, Abuhashem A, Cavaliere P, Aronson B, Shah V, Dephoure N, Stadtfeld M, Tsirigos A, Apostolou E. KLF4 is involved in the organization and regulation of pluripotency-associated three-dimensional enhancer networks. Nat Cell Biol 2019; 21:1179-1190. [PMID: 31548608 PMCID: PMC7339746 DOI: 10.1038/s41556-019-0390-6] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 08/16/2019] [Indexed: 01/24/2023]
Abstract
Cell fate transitions are accompanied by global transcriptional, epigenetic and topological changes driven by transcription factors, as is exemplified by reprogramming somatic cells to pluripotent stem cells through the expression of OCT4, KLF4, SOX2 and cMYC. How transcription factors orchestrate the complex molecular changes around their target gene loci remains incompletely understood. Here, using KLF4 as a paradigm, we provide a transcription-factor-centric view of chromatin reorganization and its association with three-dimensional enhancer rewiring and transcriptional changes during the reprogramming of mouse embryonic fibroblasts to pluripotent stem cells. Inducible depletion of KLF factors in PSCs caused a genome-wide decrease in enhancer connectivity, whereas disruption of individual KLF4 binding sites within pluripotent-stem-cell-specific enhancers was sufficient to impair enhancer-promoter contacts and reduce the expression of associated genes. Our study provides an integrative view of the complex activities of a lineage-specifying transcription factor and offers novel insights into the nature of the molecular events that follow transcription factor binding.
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Affiliation(s)
- Dafne Campigli Di Giammartino
- Sanford I Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Andreas Kloetgen
- Department of Pathology, NYU School of Medicine, New York, NY, USA
| | - Alexander Polyzos
- Sanford I Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Yiyuan Liu
- Sanford I Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Daleum Kim
- Sanford I Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Dylan Murphy
- Sanford I Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Abderhman Abuhashem
- Sanford I Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.,Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill-Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD program, New York, NY, USA
| | - Paola Cavaliere
- Department of Biochemistry, Sandra and Edward Meyer Cancer Center, Weill Cornell Medical College, New York, NY, USA
| | - Boaz Aronson
- Sanford I Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Veevek Shah
- Sanford I Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Noah Dephoure
- Department of Biochemistry, Sandra and Edward Meyer Cancer Center, Weill Cornell Medical College, New York, NY, USA
| | - Matthias Stadtfeld
- Sanford I Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.,Skirball Institute of Biomolecular Medicine, Department of Cell Biology and Helen L. and Martin S. Kimmel Center for Biology and Medicine, NYU School of Medicine, New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, NYU School of Medicine, New York, NY, USA. .,Laura and Isaac Perlmutter Cancer Center and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY, USA. .,Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY, USA.
| | - Effie Apostolou
- Sanford I Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
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18
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Berger A, Brady NJ, Bareja R, Robinson B, Conteduca V, Augello MA, Puca L, Ahmed A, Dardenne E, Lu X, Hwang I, Bagadion AM, Sboner A, Elemento O, Paik J, Yu J, Barbieri CE, Dephoure N, Beltran H, Rickman DS. N-Myc-mediated epigenetic reprogramming drives lineage plasticity in advanced prostate cancer. J Clin Invest 2019; 129:3924-3940. [PMID: 31260412 DOI: 10.1172/jci127961] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Despite recent therapeutic advances, prostate cancer remains a leading cause of cancer-related death. A subset of castration resistant prostate cancers become androgen receptor (AR) signaling-independent and develop neuroendocrine prostate cancer (NEPC) features through lineage plasticity. These NEPC tumors, associated with aggressive disease and poor prognosis, are driven, in part, by aberrant expression of N-Myc, through mechanisms that remain unclear. Integrative analysis of the N-Myc transcriptome, cistrome and interactome using in vivo, in vitro and ex vivo models (including patient-derived organoids) identified a lineage switch towards a neural identity associated with epigenetic reprogramming. N-Myc and known AR-co-factors (e.g., FOXA1 and HOXB13) overlapped, independently of AR, at genomic loci implicated in neural lineage specification. Moreover, histone marks specifically associated with lineage-defining genes were reprogrammed by N-Myc. We also demonstrated that the N-Myc-induced molecular program accurately classifies our cohort of patients with advanced prostate cancer. Finally, we revealed the potential for EZH2 inhibition to reverse the N-Myc-induced suppression of epithelial lineage genes. Altogether, our data provide insights on how N-Myc regulates lineage plasticity and epigenetic reprogramming associated with lineage-specification. The N-Myc signature we defined could also help predict the evolution of prostate cancer and thus better guide the choice of future therapeutic strategies.
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Affiliation(s)
| | | | - Rohan Bareja
- Caryl and Israel Englander Institute for Precision Medicine, NewYork-Presbyterian Hospital
| | - Brian Robinson
- Department of Pathology and Laboratory Medicine.,Caryl and Israel Englander Institute for Precision Medicine, NewYork-Presbyterian Hospital
| | | | | | | | - Adnan Ahmed
- Department of Biochemistry, Weill Cornell Medicine, New York, New York, USA
| | | | - Xiaodong Lu
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Inah Hwang
- Department of Pathology and Laboratory Medicine
| | | | - Andrea Sboner
- Department of Pathology and Laboratory Medicine.,Caryl and Israel Englander Institute for Precision Medicine, NewYork-Presbyterian Hospital.,Department of Physiology and Biophysics, Institute for Computational Biomedicine, and.,Meyer Cancer Center, Weill Cornell Medicine, New York, New York, USA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, NewYork-Presbyterian Hospital.,Department of Physiology and Biophysics, Institute for Computational Biomedicine, and.,Meyer Cancer Center, Weill Cornell Medicine, New York, New York, USA
| | - Jihye Paik
- Department of Pathology and Laboratory Medicine.,Meyer Cancer Center, Weill Cornell Medicine, New York, New York, USA
| | - Jindan Yu
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Christopher E Barbieri
- Caryl and Israel Englander Institute for Precision Medicine, NewYork-Presbyterian Hospital.,Department of Urology, and.,Meyer Cancer Center, Weill Cornell Medicine, New York, New York, USA
| | - Noah Dephoure
- Department of Biochemistry, Weill Cornell Medicine, New York, New York, USA.,Meyer Cancer Center, Weill Cornell Medicine, New York, New York, USA
| | - Himisha Beltran
- Caryl and Israel Englander Institute for Precision Medicine, NewYork-Presbyterian Hospital.,Department of Medicine.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - David S Rickman
- Department of Pathology and Laboratory Medicine.,Caryl and Israel Englander Institute for Precision Medicine, NewYork-Presbyterian Hospital.,Meyer Cancer Center, Weill Cornell Medicine, New York, New York, USA
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19
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Kikani CK, Wu X, Fogarty S, Kang SAW, Dephoure N, Gygi SP, Sabatini DM, Rutter J. Activation of PASK by mTORC1 is required for the onset of the terminal differentiation program. Proc Natl Acad Sci U S A 2019; 116:10382-10391. [PMID: 31072927 PMCID: PMC6534978 DOI: 10.1073/pnas.1804013116] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
During skeletal muscle regeneration, muscle stem cells (MuSCs) respond to multiple signaling inputs that converge onto mammalian target of rapamycin complex 1 (mTORC1) signaling pathways. mTOR function is essential for establishment of the differentiation-committed progenitors (early stage of differentiation, marked by the induction of myogenin expression), myotube fusion, and, ultimately, hypertrophy (later stage of differentiation). While a major mTORC1 substrate, p70S6K, is required for myotube fusion and hypertrophy, an mTORC1 effector for the induction of myogenin expression remains unclear. Here, we identified Per-Arnt-Sim domain kinase (PASK) as a downstream phosphorylation target of mTORC1 in MuSCs during differentiation. We have recently shown that the PASK phosphorylates Wdr5 to stimulate MuSC differentiation by epigenetically activating the myogenin promoter. We show that phosphorylation of PASK by mTORC1 is required for the activation of myogenin transcription, exit from self-renewal, and induction of the myogenesis program. Our studies reveal that mTORC1-PASK signaling is required for the rise of myogenin-positive committed myoblasts (early stage of myogenesis), whereas mTORC1-S6K signaling is required for myoblast fusion (later stage of myogenesis). Thus, our discoveries allow molecular dissection of mTOR functions during different stages of the myogenesis program driven by two different substrates.
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Affiliation(s)
- Chintan K Kikani
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84132;
| | - Xiaoying Wu
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84132
| | - Sarah Fogarty
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84132
| | - Seong Anthony Woo Kang
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Noah Dephoure
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - David M Sabatini
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142
- Broad Institute of Harvard and MIT, Cambridge, MA 02142
| | - Jared Rutter
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84132;
- Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84132
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20
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Augello MA, Liu D, Deonarine LD, Robinson BD, Huang D, Stelloo S, Blattner M, Doane AS, Wong EWP, Chen Y, Rubin MA, Beltran H, Elemento O, Bergman AM, Zwart W, Sboner A, Dephoure N, Barbieri CE. CHD1 Loss Alters AR Binding at Lineage-Specific Enhancers and Modulates Distinct Transcriptional Programs to Drive Prostate Tumorigenesis. Cancer Cell 2019; 35:817-819. [PMID: 31085180 DOI: 10.1016/j.ccell.2019.04.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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21
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Augello MA, Liu D, Deonarine LD, Robinson BD, Huang D, Stelloo S, Blattner M, Doane AS, Wong EWP, Chen Y, Rubin MA, Beltran H, Elemento O, Bergman AM, Zwart W, Sboner A, Dephoure N, Barbieri CE. CHD1 Loss Alters AR Binding at Lineage-Specific Enhancers and Modulates Distinct Transcriptional Programs to Drive Prostate Tumorigenesis. Cancer Cell 2019; 35:603-617.e8. [PMID: 30930119 PMCID: PMC6467783 DOI: 10.1016/j.ccell.2019.03.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/06/2018] [Accepted: 02/28/2019] [Indexed: 12/11/2022]
Abstract
Deletion of the gene encoding the chromatin remodeler CHD1 is among the most common alterations in prostate cancer (PCa); however, the tumor-suppressive functions of CHD1 and reasons for its tissue-specific loss remain undefined. We demonstrated that CHD1 occupied prostate-specific enhancers enriched for the androgen receptor (AR) and lineage-specific cofactors. Upon CHD1 loss, the AR cistrome was redistributed in patterns consistent with the oncogenic AR cistrome in PCa samples and drove tumor formation in the murine prostate. Notably, this cistrome shift was associated with a unique AR transcriptional signature enriched for pro-oncogenic pathways unique to this tumor subclass. Collectively, these data credential CHD1 as a tumor suppressor in the prostate that constrains AR binding/function to limit tumor progression.
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Affiliation(s)
- Michael A Augello
- Department of Urology, Weill Cornell Medicine, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Deli Liu
- Department of Urology, Weill Cornell Medicine, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Lesa D Deonarine
- Department of Urology, Weill Cornell Medicine, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Brian D Robinson
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Dennis Huang
- Department of Urology, Weill Cornell Medicine, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Suzan Stelloo
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Mirjam Blattner
- Department of Urology, Weill Cornell Medicine, New York, NY 10065, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ashley S Doane
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Elissa W P Wong
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yu Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mark A Rubin
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Himisha Beltran
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Olivier Elemento
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andries M Bergman
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Division of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands; Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Andrea Sboner
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Noah Dephoure
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA
| | - Christopher E Barbieri
- Department of Urology, Weill Cornell Medicine, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA.
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22
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Hwang S, Gustafsson HT, O'Sullivan C, Bisceglia G, Huang X, Klose C, Schevchenko A, Dickson RC, Cavaliere P, Dephoure N, Torres EM. Serine-Dependent Sphingolipid Synthesis Is a Metabolic Liability of Aneuploid Cells. Cell Rep 2019; 21:3807-3818. [PMID: 29281829 DOI: 10.1016/j.celrep.2017.11.103] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 11/06/2017] [Accepted: 11/29/2017] [Indexed: 10/18/2022] Open
Abstract
Aneuploidy disrupts cellular homeostasis. However, the molecular mechanisms underlying the physiological responses and adaptation to aneuploidy are not well understood. Deciphering these mechanisms is important because aneuploidy is associated with diseases, including intellectual disability and cancer. Although tumors and mammalian aneuploid cells, including several cancer cell lines, show altered levels of sphingolipids, the role of sphingolipids in aneuploidy remains unknown. Here, we show that ceramides and long-chain bases, sphingolipid molecules that slow proliferation and promote survival, are increased by aneuploidy. Sphingolipid levels are tightly linked to serine synthesis, and inhibiting either serine or sphingolipid synthesis can specifically impair the fitness of aneuploid cells. Remarkably, the fitness of aneuploid cells improves or deteriorates upon genetically decreasing or increasing ceramides, respectively. Combined targeting of serine and sphingolipid synthesis could be exploited to specifically target cancer cells, the vast majority of which are aneuploid.
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Affiliation(s)
- Sunyoung Hwang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - H Tobias Gustafsson
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ciara O'Sullivan
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Gianna Bisceglia
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Xinhe Huang
- Department of Molecular and Cellular Biochemistry and the Lucille Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40506, USA
| | - Christian Klose
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Andrej Schevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Robert C Dickson
- Department of Molecular and Cellular Biochemistry and the Lucille Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40506, USA
| | - Paola Cavaliere
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10021, USA
| | - Noah Dephoure
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10021, USA
| | - Eduardo M Torres
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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23
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Boehm KM, Bhinder B, Raja VJ, Dephoure N, Elemento O. Predicting peptide presentation by major histocompatibility complex class I: an improved machine learning approach to the immunopeptidome. BMC Bioinformatics 2019; 20:7. [PMID: 30611210 PMCID: PMC6321722 DOI: 10.1186/s12859-018-2561-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 12/06/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND To further our understanding of immunopeptidomics, improved tools are needed to identify peptides presented by major histocompatibility complex class I (MHC-I). Many existing tools are limited by their reliance upon chemical affinity data, which is less biologically relevant than sampling by mass spectrometry, and other tools are limited by incomplete exploration of machine learning approaches. Herein, we assemble publicly available data describing human peptides discovered by sampling the MHC-I immunopeptidome with mass spectrometry and use this database to train random forest classifiers (ForestMHC) to predict presentation by MHC-I. RESULTS As measured by precision in the top 1% of predictions, our method outperforms NetMHC and NetMHCpan on test sets, and it outperforms both these methods and MixMHCpred on new data from an ovarian carcinoma cell line. We also find that random forest scores correlate monotonically, but not linearly, with known chemical binding affinities, and an information-based analysis of classifier features shows the importance of anchor positions for our classification. The random-forest approach also outperforms a deep neural network and a convolutional neural network trained on identical data. Finally, we use our large database to confirm that gene expression partially determines peptide presentation. CONCLUSIONS ForestMHC is a promising method to identify peptides bound by MHC-I. We have demonstrated the utility of random forest-based approaches in predicting peptide presentation by MHC-I, assembled the largest known database of MS binding data, and mined this database to show the effect of gene expression on peptide presentation. ForestMHC has potential applicability to basic immunology, rational vaccine design, and neoantigen binding prediction for cancer immunotherapy. This method is publicly available for applications and further validation.
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Affiliation(s)
- Kevin Michael Boehm
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, 1300 York Avenue, New York, NY USA
| | - Bhavneet Bhinder
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medical College, 413 East 69th Street, New York, NY USA
- Institute for Computational Biomedicine, Weill Cornell Medical College, 1305 York Avenue, New York, NY USA
| | - Vijay Joseph Raja
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, NY USA
| | - Noah Dephoure
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, NY USA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medical College, 413 East 69th Street, New York, NY USA
- Institute for Computational Biomedicine, Weill Cornell Medical College, 1305 York Avenue, New York, NY USA
- Meyer Cancer Center, Weill Cornell Medical College, 1300 York Avenue, New York, NY USA
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24
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Affiliation(s)
- Adnan Ahmed
- Department of Biochemistry, Sandra and Edward Meyer Cancer Center, Weill Cornell Medical College, New York, New York 10021, United States
| | - Vijay J. Raja
- Department of Biochemistry, Sandra and Edward Meyer Cancer Center, Weill Cornell Medical College, New York, New York 10021, United States
| | - Paola Cavaliere
- Department of Biochemistry, Sandra and Edward Meyer Cancer Center, Weill Cornell Medical College, New York, New York 10021, United States
| | - Noah Dephoure
- Department of Biochemistry, Sandra and Edward Meyer Cancer Center, Weill Cornell Medical College, New York, New York 10021, United States
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25
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Clarke J, Dephoure N, Horecka I, Gygi S, Kellogg D. A conserved signaling network monitors delivery of sphingolipids to the plasma membrane in budding yeast. Mol Biol Cell 2017; 28:2589-2599. [PMID: 28794263 PMCID: PMC5620368 DOI: 10.1091/mbc.e17-01-0081] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 07/28/2017] [Accepted: 08/02/2017] [Indexed: 12/16/2022] Open
Abstract
In budding yeast, signals generated in response to membrane growth are required for cell cycle progression. A mass spectrometry screen for signals triggered by an arrest of membrane growth identified sphingolipid signaling pathways. Delivery of sphingolipids to the plasma membrane could generate signals that control cell growth and the cell cycle. In budding yeast, cell cycle progression and ribosome biogenesis are dependent on plasma membrane growth, which ensures that events of cell growth are coordinated with each other and with the cell cycle. However, the signals that link the cell cycle and ribosome biogenesis to membrane growth are poorly understood. Here we used proteome-wide mass spectrometry to systematically discover signals associated with membrane growth. The results suggest that membrane trafficking events required for membrane growth generate sphingolipid-dependent signals. A conserved signaling network appears to play an essential role in signaling by responding to delivery of sphingolipids to the plasma membrane. In addition, sphingolipid-dependent signals control phosphorylation of protein kinase C (Pkc1), which plays an essential role in the pathways that link the cell cycle and ribosome biogenesis to membrane growth. Together these discoveries provide new clues as to how growth-dependent signals control cell growth and the cell cycle.
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Affiliation(s)
- Jesse Clarke
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Noah Dephoure
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10021
| | - Ira Horecka
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Steven Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Douglas Kellogg
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064
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26
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Yoon SO, Shin S, Karreth FA, Buel GR, Jedrychowski MP, Plas DR, Dedhar S, Gygi SP, Roux PP, Dephoure N, Blenis J. Focal Adhesion- and IGF1R-Dependent Survival and Migratory Pathways Mediate Tumor Resistance to mTORC1/2 Inhibition. Mol Cell 2017; 67:512-527.e4. [PMID: 28757207 DOI: 10.1016/j.molcel.2017.06.033] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/24/2017] [Accepted: 06/27/2017] [Indexed: 01/22/2023]
Abstract
Aberrant signaling by the mammalian target of rapamycin (mTOR) contributes to the devastating features of cancer cells. Thus, mTOR is a critical therapeutic target and catalytic inhibitors are being investigated as anti-cancer drugs. Although mTOR inhibitors initially block cell proliferation, cell viability and migration in some cancer cells are quickly restored. Despite sustained inhibition of mTORC1/2 signaling, Akt, a kinase regulating cell survival and migration, regains phosphorylation at its regulatory sites. Mechanistically, mTORC1/2 inhibition promotes reorganization of integrin/focal adhesion kinase-mediated adhesomes, induction of IGFR/IR-dependent PI3K activation, and Akt phosphorylation via an integrin/FAK/IGFR-dependent process. This resistance mechanism contributes to xenograft tumor cell growth, which is prevented with mTOR plus IGFR inhibitors, supporting this combination as a therapeutic approach for cancers.
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Affiliation(s)
- Sang-Oh Yoon
- Department of Pharmacology, Meyer Cancer Center, Weill Cornell Medical College, New York, NY 10065, USA.
| | - Sejeong Shin
- Department of Pharmacology, Meyer Cancer Center, Weill Cornell Medical College, New York, NY 10065, USA
| | - Florian A Karreth
- Department of Medicine, Meyer Cancer Center, Weill Cornell Medical College, New York, NY 10065, USA
| | - Gwen R Buel
- Department of Pharmacology, Meyer Cancer Center, Weill Cornell Medical College, New York, NY 10065, USA
| | | | - David R Plas
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Shoukat Dedhar
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Philippe P Roux
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Noah Dephoure
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065, USA
| | - John Blenis
- Department of Pharmacology, Meyer Cancer Center, Weill Cornell Medical College, New York, NY 10065, USA.
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27
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Cornish-Bowden A, Cornish-Bowden A, Rasnick D, Heng HH, Horne S, Abdallah B, Liu G, Ye CJ, Bloomfield M, Vincent MD, Aldaz CM, Karlsson J, Valind A, Jansson C, Gisselsson D, Graves JAM, Stepanenko AA, Andreieva SV, Korets KV, Mykytenko DO, Huleyuk NL, Baklaushev VP, Kovaleva OA, Chekhonin VP, Vassetzky YS, Avdieiev SS, Bakker B, Taudt AS, Belderbos ME, Porubsky D, Spierings DCJ, de Jong TV, Halsema N, Kazemier HG, Hoekstra-Wakker K, Bradley A, de Bont ESJM, van den Berg A, Guryev V, Lansdorp PM, Tatché MC, Foijer F, Liehr T, Baudoin NC, Nicholson JM, Soto K, Quintanilla I, Camps J, Cimini D, Dürrbaum M, Donnelly N, Passerini V, Kruse C, Habermann B, Storchová Z, Mandrioli D, Belpoggi F, Silbergeld EK, Perry MJ, Skotheim RI, Løvf M, Johannessen B, Hoff AM, Zhao S, SveeStrømme JM, Sveen A, Lothe RA, Hehlmann R, Voskanyan A, Fabarius A, Böcking A, Biesterfeld S, Berynskyy L, Börgermann C, Engers R, Dietz J, Fritz A, Sehgal N, Vecerova J, Stojkovicz B, Ding H, Page N, Tye C, Bhattacharya S, Xu J, Stein G, Stein J, Berezney R, Gong X, Grasedieck S, Swoboda J, Rücker FG, Bullinger L, Pollack JR, Roumelioti FM, Chiourea M, Raftopoulou C, Gagos S, Duesberg P, Bloomfield M, Hwang S, Gustafsson HT, O’Sullivan C, Acevedo-Colina A, Huang X, Klose C, Schevchenko A, Dickson RC, Cavaliere P, Dephoure N, Torres EM, Stampfer MR, Vrba L, LaBarge MA, Futscher B, Garbe JC, Zhou YH, Trinh AL, Zhou YH, Digman M. Abstracts from the 3rd Conference on Aneuploidy and Cancer: Clinical and Experimental Aspects. Mol Cytogenet 2017. [PMCID: PMC5499067 DOI: 10.1186/s13039-017-0320-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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28
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Huang FK, Zhang G, Lawlor K, Nazarian A, Philip J, Tempst P, Dephoure N, Neubert TA. Deep Coverage of Global Protein Expression and Phosphorylation in Breast Tumor Cell Lines Using TMT 10-plex Isobaric Labeling. J Proteome Res 2017; 16:1121-1132. [PMID: 28102081 DOI: 10.1021/acs.jproteome.6b00374] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Labeling peptides with isobaric tags is a popular strategy in quantitative bottom-up proteomics. In this study, we labeled six breast tumor cell lysates (1.34 mg proteins per channel) using 10-plex tandem mass tag reagents and analyzed the samples on a Q Exactive HF Quadrupole-Orbitrap mass spectrometer. We identified a total of 8,706 proteins and 28,186 phosphopeptides, including 7,394 proteins and 23,739 phosphosites common to all channels. The majority of technical replicates correlated with a R2 ≥ 0.98, indicating minimum variability was introduced after labeling. Unsupervised hierarchical clustering of phosphopeptide data sets successfully classified the breast tumor samples into Her2 (epidermal growth factor receptor 2) positive and Her2 negative groups, whereas mRNA abundance did not. The tyrosine phosphorylation levels of receptor tyrosine kinases, phosphoinositide-3-kinase, protein kinase C delta, and Src homology 2, among others, were significantly higher in the Her2 positive than the Her2 negative group. Despite ratio compression in MS2-based experiments, we demonstrated the ratios calculated using an MS2 method are highly correlated (R2 > 0.65) with ratios obtained using MS3-based quantitation (using a Thermo Orbitrap Fusion mass spectrometer) with reduced ratio suppression. Given the deep coverage of global and phosphoproteomes, our data show that MS2-based quantitation using TMT can be successfully used for large-scale multiplexed quantitative proteomics.
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Affiliation(s)
- Fang-Ke Huang
- Kimmel Center for Biology and Medicine at the Skirball Institute, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine , New York, New York 10016, United States
| | - Guoan Zhang
- Kimmel Center for Biology and Medicine at the Skirball Institute, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine , New York, New York 10016, United States
| | - Kevin Lawlor
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United States
| | - Arpi Nazarian
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United States
| | - John Philip
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United States
| | - Paul Tempst
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United States
| | - Noah Dephoure
- Sandra and Edward Meyer Cancer Center, Department of Biochemistry, Weill Cornell Medical College , New York, New York 10065, United States
| | - Thomas A Neubert
- Kimmel Center for Biology and Medicine at the Skirball Institute, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine , New York, New York 10016, United States
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29
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Thai V, Dephoure N, Weiss A, Ferguson J, Leitao R, Gygi SP, Kellogg DR. Protein Kinase C Controls Binding of Igo/ENSA Proteins to Protein Phosphatase 2A in Budding Yeast. J Biol Chem 2017; 292:4925-4941. [PMID: 28100785 DOI: 10.1074/jbc.m116.753004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 01/09/2017] [Indexed: 11/06/2022] Open
Abstract
Protein phosphatase 2A (PP2A) plays important roles in controlling mitosis in all eukaryotic cells. The form of PP2A that controls mitosis is associated with a conserved regulatory subunit that is called B55 in vertebrates and Cdc55 in budding yeast. The activity of this form of PP2A can be inhibited by binding of conserved Igo/ENSA proteins. Although the mechanisms that activate Igo/ENSA to bind and inhibit PP2A are well understood, little is known about how Igo/Ensa are inactivated. Here, we have analyzed regulation of Igo/ENSA in the context of a checkpoint pathway that links mitotic entry to membrane growth in budding yeast. Protein kinase C (Pkc1) relays signals in the pathway by activating PP2ACdc55 We discovered that constitutively active Pkc1 can drive cells through a mitotic checkpoint arrest, which suggests that Pkc1-dependent activation of PP2ACdc55 plays a critical role in checkpoint signaling. We therefore used mass spectrometry to determine how Pkc1 modifies the PP2ACdc55 complex. This revealed that Pkc1 induces changes in the phosphorylation of multiple subunits of the complex, as well as dissociation of Igo/ENSA. Pkc1 directly phosphorylates Cdc55 and Igo/ENSA, and phosphorylation site mapping and mutagenesis indicate that phosphorylation of Cdc55 contributes to Igo/ENSA dissociation. Association of Igo2 with PP2ACdc55 is regulated during the cell cycle, yet mutation of Pkc1-dependent phosphorylation sites on Cdc55 and Igo2 did not cause defects in mitotic progression. Together, the data suggest that Pkc1 controls PP2ACdc55 by multiple overlapping mechanisms.
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Affiliation(s)
- Vu Thai
- From the Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064
| | - Noah Dephoure
- the Department of Biochemistry, Weill Cornell Medical College, New York, New York 10021, and
| | - Amit Weiss
- From the Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064
| | - Jacqueline Ferguson
- From the Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064
| | - Ricardo Leitao
- From the Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064
| | - Steven P Gygi
- the Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Douglas R Kellogg
- From the Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064,
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30
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Ron-Harel N, Santos D, Ghergurovich JM, Sage PT, Reddy A, Lovitch SB, Dephoure N, Satterstrom FK, Sheffer M, Spinelli JB, Gygi S, Rabinowitz JD, Sharpe AH, Haigis MC. Mitochondrial Biogenesis and Proteome Remodeling Promote One-Carbon Metabolism for T Cell Activation. Cell Metab 2016; 24:104-17. [PMID: 27411012 PMCID: PMC5330619 DOI: 10.1016/j.cmet.2016.06.007] [Citation(s) in RCA: 252] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 04/12/2016] [Accepted: 06/10/2016] [Indexed: 01/06/2023]
Abstract
Naive T cell stimulation activates anabolic metabolism to fuel the transition from quiescence to growth and proliferation. Here we show that naive CD4(+) T cell activation induces a unique program of mitochondrial biogenesis and remodeling. Using mass spectrometry, we quantified protein dynamics during T cell activation. We identified substantial remodeling of the mitochondrial proteome over the first 24 hr of T cell activation to generate mitochondria with a distinct metabolic signature, with one-carbon metabolism as the most induced pathway. Salvage pathways and mitochondrial one-carbon metabolism, fed by serine, contribute to purine and thymidine synthesis to enable T cell proliferation and survival. Genetic inhibition of the mitochondrial serine catabolic enzyme SHMT2 impaired T cell survival in culture and antigen-specific T cell abundance in vivo. Thus, during T cell activation, mitochondrial proteome remodeling generates specialized mitochondria with enhanced one-carbon metabolism that is critical for T cell activation and survival.
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Affiliation(s)
- Noga Ron-Harel
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Santos
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Jonathan M Ghergurovich
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Peter T Sage
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Anita Reddy
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Scott B Lovitch
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Noah Dephoure
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - F Kyle Satterstrom
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Michal Sheffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jessica B Spinelli
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Steven Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joshua D Rabinowitz
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Arlene H Sharpe
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Marcia C Haigis
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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31
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Lucena R, Dephoure N, Gygi SP, Kellogg DR, Tallada VA, Daga RR, Jimenez J. Nucleocytoplasmic transport in the midzone membrane domain controls yeast mitotic spindle disassembly. ACTA ACUST UNITED AC 2015; 209:387-402. [PMID: 25963819 PMCID: PMC4427787 DOI: 10.1083/jcb.201412144] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
During anaphase B, Imp1-mediated transport of the AAA-ATPase Cdc48 protein at the membrane domain surrounding the mitotic spindle midzone promotes spindle midzone dissolution in fission yeast. During each cell cycle, the mitotic spindle is efficiently assembled to achieve chromosome segregation and then rapidly disassembled as cells enter cytokinesis. Although much has been learned about assembly, how spindles disassemble at the end of mitosis remains unclear. Here we demonstrate that nucleocytoplasmic transport at the membrane domain surrounding the mitotic spindle midzone, here named the midzone membrane domain (MMD), is essential for spindle disassembly in Schizosaccharomyces pombe cells. We show that, during anaphase B, Imp1-mediated transport of the AAA-ATPase Cdc48 protein at the MMD allows this disassembly factor to localize at the spindle midzone, thereby promoting spindle midzone dissolution. Our findings illustrate how a separate membrane compartment supports spindle disassembly in the closed mitosis of fission yeast.
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Affiliation(s)
- Rafael Lucena
- Centro Andaluz de Biología del Desarrollo. Universidad Pablo de Olavide/Consejo Superior de Investigaciones Cientificas, 41013 Sevilla, Spain Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Noah Dephoure
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Steve P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Douglas R Kellogg
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Victor A Tallada
- Centro Andaluz de Biología del Desarrollo. Universidad Pablo de Olavide/Consejo Superior de Investigaciones Cientificas, 41013 Sevilla, Spain
| | - Rafael R Daga
- Centro Andaluz de Biología del Desarrollo. Universidad Pablo de Olavide/Consejo Superior de Investigaciones Cientificas, 41013 Sevilla, Spain
| | - Juan Jimenez
- Centro Andaluz de Biología del Desarrollo. Universidad Pablo de Olavide/Consejo Superior de Investigaciones Cientificas, 41013 Sevilla, Spain
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32
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Elia AEH, Boardman AP, Wang DC, Huttlin EL, Everley RA, Dephoure N, Zhou C, Koren I, Gygi SP, Elledge SJ. Quantitative Proteomic Atlas of Ubiquitination and Acetylation in the DNA Damage Response. Mol Cell 2015; 59:867-81. [PMID: 26051181 DOI: 10.1016/j.molcel.2015.05.006] [Citation(s) in RCA: 243] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 03/17/2015] [Accepted: 04/29/2015] [Indexed: 01/06/2023]
Abstract
Execution of the DNA damage response (DDR) relies upon a dynamic array of protein modifications. Using quantitative proteomics, we have globally profiled ubiquitination, acetylation, and phosphorylation in response to UV and ionizing radiation. To improve acetylation site profiling, we developed the strategy FACET-IP. Our datasets of 33,500 ubiquitination and 16,740 acetylation sites provide valuable insight into DDR remodeling of the proteome. We find that K6- and K33-linked polyubiquitination undergo bulk increases in response to DNA damage, raising the possibility that these linkages are largely dedicated to DDR function. We also show that Cullin-RING ligases mediate 10% of DNA damage-induced ubiquitination events and that EXO1 is an SCF-Cyclin F substrate in the response to UV radiation. Our extensive datasets uncover additional regulated sites on known DDR players such as PCNA and identify previously unknown DDR targets such as CENPs, underscoring the broad impact of the DDR on cellular physiology.
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Affiliation(s)
- Andrew E H Elia
- Department of Genetics, Harvard Medical School; Division of Genetics, Brigham and Women's Hospital; Howard Hughes Medical Institute, Boston, MA 02115, USA; Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Alexander P Boardman
- Department of Genetics, Harvard Medical School; Division of Genetics, Brigham and Women's Hospital; Howard Hughes Medical Institute, Boston, MA 02115, USA; Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - David C Wang
- Department of Genetics, Harvard Medical School; Division of Genetics, Brigham and Women's Hospital; Howard Hughes Medical Institute, Boston, MA 02115, USA; Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Edward L Huttlin
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert A Everley
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Noah Dephoure
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Chunshui Zhou
- Department of Genetics, Harvard Medical School; Division of Genetics, Brigham and Women's Hospital; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Itay Koren
- Department of Genetics, Harvard Medical School; Division of Genetics, Brigham and Women's Hospital; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Stephen J Elledge
- Department of Genetics, Harvard Medical School; Division of Genetics, Brigham and Women's Hospital; Howard Hughes Medical Institute, Boston, MA 02115, USA.
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33
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Xu H, Dephoure N, Sun H, Zhang H, Fan F, Liu J, Ning X, Dai S, Liu B, Gao M, Fu S, Gygi SP, Zhou C. Proteomic Profiling of Paclitaxel Treated Cells Identifies a Novel Mechanism of Drug Resistance Mediated by PDCD4. J Proteome Res 2015; 14:2480-91. [PMID: 25928036 DOI: 10.1021/acs.jproteome.5b00004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Paclitaxel (PTX) is a widely used chemotherapeutic drug effective against numerous cancers. To elucidate cellular pathways targeted by PTX and identify novel mechanisms of PTX resistance, we used a SILAC based quantitative proteomic approach to evaluate global changes of cellular protein abundance in HeLa cells. We identified 347 proteins involved in a number of biological processes including spindle assembly, mitotic exit, and extracellular adhesion whose abundance changes upon PTX treatment. Notably, the tumor suppressor PDCD4 involved in translation suppression was down-regulated by PTX. We demonstrated that PDCD4 is a cell-cycle regulated protein and that changes in its abundance are sufficient to alter PTX sensitivity in multiple human cancer cell lines. Immunoprecipitation of PDCD4-RNA complexes and RT-PCR revealed that PDCD4 mediated PTX sensitivity acts through its interaction with mRNA of UBE2S, a ubiquitin K11 linkage conjugating enzyme critical for mitotic exit. Lastly, high levels of PDCD4 in lung cancer tissues are positively correlated with the longer overall survival time of the examined lung cancer patients with PTX involved adjuvant therapy. Therefore, our proteomic screen for paclitaxel targets not only provided novel insight into the cellular resistance to paclitaxel via the PDCD4-mitotic exit regulation axis, but also offered a predictive biomarker for paclitaxel-based personalized chemotherapy in the treatment of lung cancer.
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Affiliation(s)
- Hui Xu
- †The Laboratory of Medical Genetics, Harbin Medical University, Harbin, China 150081
| | - Noah Dephoure
- ‡Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Huiying Sun
- †The Laboratory of Medical Genetics, Harbin Medical University, Harbin, China 150081
| | - Haiyuan Zhang
- †The Laboratory of Medical Genetics, Harbin Medical University, Harbin, China 150081
| | - Fangfang Fan
- †The Laboratory of Medical Genetics, Harbin Medical University, Harbin, China 150081
| | - Jiawei Liu
- †The Laboratory of Medical Genetics, Harbin Medical University, Harbin, China 150081
| | - Xuelian Ning
- †The Laboratory of Medical Genetics, Harbin Medical University, Harbin, China 150081
| | - Shaochun Dai
- §The Tumor Hospital, Harbin Medical University, Harbin, China 150081
| | - Baogang Liu
- §The Tumor Hospital, Harbin Medical University, Harbin, China 150081
| | - Min Gao
- ∥The Fourth Affiliated Hospital, Harbin Medical University, Harbin, China 150001
| | - Songbin Fu
- †The Laboratory of Medical Genetics, Harbin Medical University, Harbin, China 150081
| | - Steven P Gygi
- ‡Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Chunshui Zhou
- †The Laboratory of Medical Genetics, Harbin Medical University, Harbin, China 150081
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Westbrook TF, Nair A, Sun T, Karlin KL, Kessler J, Migliaccio I, Nguyen DX, Bernardi RJ, Renwick A, Creighton CJ, Dephoure N, Gygi SP, Shaw CA, Gibbs R, Wheeler D, Schiff R, Christensen JG, Shields DJ, Osborne CK, Elledge SJ, Hilsenbeck SG, Lewis MT. Abstract P6-11-01: A broad spectrum therapeutic strategy for TNBC revealed by a new pathway that coordinates oncogenic RTKs. Cancer Res 2015. [DOI: 10.1158/1538-7445.sabcs14-p6-11-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Triple-negative breast cancer (TNBC) is a collection of diseases with distinct clinical behaviors and heterogeneous molecular features. Such clinical and genetic heterogeneity has called into question whether there are common pathogenic mechanisms (and potential therapeutic targets) driving the TNBC subtype of breast cancer. Herein, we present evidence of a novel tumor suppressor network that is frequently compromised in TNBC, and a broadly-effective strategy to target this pathway for TNBC therapeutic intervention. Using an unbiased genetic screen, we identified a tumor suppressor network governing tumor survival of TNBCs in vitro and in vivo. We define the tyrosine phosphatase PTPN12 as a core component in this network. PTPN12 is a potent suppressor of mammary epithelial cell survival and transformation, and PTPN12 function is compromised in more than 70% of human TNBCs. Notably, the tumorigenic and metastatic potential of PTPN12-deficient TNBCs is severely impaired by restoring PTPN12, suggesting that strategies to mimic PTPN12 function have substantive therapeutic potential. Using integrative proteomic, genetic, and pharmacologic approaches, we demonstrate that PTPN12 suppresses TNBC survival by inhibiting multiple oncogenic receptor tyrosine kinases (TKs) including MET, PDGFRβ, and others. Frequent inactivation of PTPN12 in human TNBC unleashes these oncogenic TKs in a concerted manner. Importantly, combination inhibitors targeting these PTPN12-regulated TKs significantly impair TNBC cell survival and confer robust tumor regression across a panel of 18 patient-derived xenograft ("PDX") models of human TNBC. This suggests that TNBCs are broadly dependent on a distinct combination of proto-oncogenic tyrosine kinases constrained by PTPN12. Collectively, these data identify PTPN12 as a commonly inactivated tumor suppressor in TNBC and provide a rationale for combinatorially targeting select receptor tyrosine kinases in TNBC and other cancers based on their defects in tyrosine phosphatase activity.
Citation Format: Thomas F Westbrook, Amritha Nair, Tingting Sun, Kristen L Karlin, Jessica Kessler, Ilenia Migliaccio, Don X Nguyen, Ronald J Bernardi, Alex Renwick, Chad J Creighton, Noah Dephoure, Steven P Gygi, Chad A Shaw, Richard Gibbs, David Wheeler, Rachel Schiff, James G Christensen, David J Shields, C Kent Osborne, Stephen J Elledge, Susan G Hilsenbeck, Michael T Lewis. A broad spectrum therapeutic strategy for TNBC revealed by a new pathway that coordinates oncogenic RTKs [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P6-11-01.
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35
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Van Vranken JG, Bricker DK, Dephoure N, Gygi SP, Cox JE, Thummel CS, Rutter J. SDHAF4 promotes mitochondrial succinate dehydrogenase activity and prevents neurodegeneration. Cell Metab 2014; 20:241-52. [PMID: 24954416 PMCID: PMC4126880 DOI: 10.1016/j.cmet.2014.05.012] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 03/28/2014] [Accepted: 04/28/2014] [Indexed: 02/05/2023]
Abstract
Succinate dehydrogenase (SDH) occupies a central place in cellular energy production, linking the tricarboxylic cycle with the electron transport chain. As a result, a subset of cancers and neuromuscular disorders result from mutations affecting any of the four SDH structural subunits or either of two known SDH assembly factors. Herein we characterize an evolutionarily conserved SDH assembly factor designated Sdh8/SDHAF4, using yeast, Drosophila, and mammalian cells. Sdh8 interacts specifically with the catalytic Sdh1 subunit in the mitochondrial matrix, facilitating its association with Sdh2 and the subsequent assembly of the SDH holocomplex. These roles for Sdh8 are critical for preventing motility defects and neurodegeneration in Drosophila as well as the excess ROS generated by free Sdh1. These studies provide insights into the mechanisms by which SDH is assembled and raise the possibility that some forms of neuromuscular disease may be associated with mutations that affect this SDH assembly factor.
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Affiliation(s)
- Jonathan G Van Vranken
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Daniel K Bricker
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Noah Dephoure
- Department of Cell Biology, Harvard University Medical School, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard University Medical School, Boston, MA 02115, USA
| | - James E Cox
- Metabolomics Core Research Facility, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Carl S Thummel
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
| | - Jared Rutter
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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36
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Dephoure N, Hwang S, O'Sullivan C, Dodgson SE, Gygi SP, Amon A, Torres EM. Quantitative proteomic analysis reveals posttranslational responses to aneuploidy in yeast. eLife 2014; 3:e03023. [PMID: 25073701 PMCID: PMC4129440 DOI: 10.7554/elife.03023] [Citation(s) in RCA: 181] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Aneuploidy causes severe developmental defects and is a near universal feature of tumor cells. Despite its profound effects, the cellular processes affected by aneuploidy are not well characterized. Here, we examined the consequences of aneuploidy on the proteome of aneuploid budding yeast strains. We show that although protein levels largely scale with gene copy number, subunits of multi-protein complexes are notable exceptions. Posttranslational mechanisms attenuate their expression when their encoding genes are in excess. Our proteomic analyses further revealed a novel aneuploidy-associated protein expression signature characteristic of altered metabolism and redox homeostasis. Indeed aneuploid cells harbor increased levels of reactive oxygen species (ROS). Interestingly, increased protein turnover attenuates ROS levels and this novel aneuploidy-associated signature and improves the fitness of most aneuploid strains. Our results show that aneuploidy causes alterations in metabolism and redox homeostasis. Cells respond to these alterations through both transcriptional and posttranscriptional mechanisms. DOI:http://dx.doi.org/10.7554/eLife.03023.001 Nearly all tumor cells contain abnormal number of chromosomes. This state is called aneuploidy, and can also cause embryos to be miscarried, or to be born with severe developmental disorders. Proteins are produced from the genes contained within chromosomes, and so cells with too many chromosomes produce too many of some proteins. How do these cells cope with this excess? Previous work identified one strategy where a gene called UBP6 is mutated to prevent it from working correctly. The UBP6 gene normally encodes a protein that removes a small tag (called ubiquitin) from other proteins. This tag normally marks other proteins that should be degraded; thus, if UBP6 is not working, more proteins are broken down. Dephoure et al. investigated the effect of aneuploidy on the proteins produced by 12 different types of yeast cell, which each had an extra chromosome. In general, the amount of each protein produced by these yeast increased depending on the number of extra copies of the matching genes found on the extra chromosome. However, this was not the case for around 20% of the proteins, which were found in lower amounts than expected. Dephoure et al. revealed that this was not because fewer proteins were made, but because more were broken down. These proteins may be targeted for degradation because they are unstable, as many of these proteins need to bind to other proteins to keep them stable—but these stabilizing proteins are not also over-produced. Aneuploidy in cells also has other effects, including changing the cells' metabolism so that the cells grow more slowly and do not respond as well to stress. However, Dephoure et al. found that, as well as reducing the number of proteins produced, deleting the UBP6 gene also increased the fitness of the cells. Targeting the protein encoded by the UBP6 gene, or others that also stop proteins being broken down, could therefore help to reduce the negative effects of aneuploidy for a cell. Whether targeting these genes or proteins could also help to treat the diseases and disorders that result from aneuploidy, such as Alzheimer's and Huntington's disease, remains to be investigated. DOI:http://dx.doi.org/10.7554/eLife.03023.002
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Affiliation(s)
- Noah Dephoure
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Sunyoung Hwang
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, United States
| | - Ciara O'Sullivan
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, United States
| | - Stacie E Dodgson
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Angelika Amon
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
| | - Eduardo M Torres
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, United States
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37
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Chen YC, Umanah GKE, Dephoure N, Andrabi SA, Gygi SP, Dawson TM, Dawson VL, Rutter J. Msp1/ATAD1 maintains mitochondrial function by facilitating the degradation of mislocalized tail-anchored proteins. EMBO J 2014; 33:1548-64. [PMID: 24843043 DOI: 10.15252/embj.201487943] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The majority of ER-targeted tail-anchored (TA) proteins are inserted into membranes by the Guided Entry of Tail-anchored protein (GET) system. Disruption of this system causes a subset of TA proteins to mislocalize to mitochondria. We show that the AAA+ ATPase Msp1 limits the accumulation of mislocalized TA proteins on mitochondria. Deletion of MSP1 causes the Pex15 and Gos1 TA proteins to accumulate on mitochondria when the GET system is impaired. Likely as a result of failing to extract mislocalized TA proteins, yeast with combined mutation of the MSP1 gene and the GET system exhibit strong synergistic growth defects and severe mitochondrial damage, including loss of mitochondrial DNA and protein and aberrant mitochondrial morphology. Like yeast Msp1, human ATAD1 limits the mitochondrial mislocalization of PEX26 and GOS28, orthologs of Pex15 and Gos1, respectively. GOS28 protein level is also increased in ATAD1(-/-) mouse tissues. Therefore, we propose that yeast Msp1 and mammalian ATAD1 are conserved members of the mitochondrial protein quality control system that might promote the extraction and degradation of mislocalized TA proteins to maintain mitochondrial integrity.
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Affiliation(s)
- Yu-Chan Chen
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City UT, USA
| | - George K E Umanah
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Noah Dephoure
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Shaida A Andrabi
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA Departments of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jared Rutter
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City UT, USA
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Zapata J, Dephoure N, Macdonough T, Yu Y, Parnell EJ, Mooring M, Gygi SP, Stillman DJ, Kellogg DR. PP2ARts1 is a master regulator of pathways that control cell size. ACTA ACUST UNITED AC 2014; 204:359-76. [PMID: 24493588 PMCID: PMC3912523 DOI: 10.1083/jcb.201309119] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Cell size checkpoints ensure that passage through G1 and mitosis occurs only when sufficient growth has occurred. The mechanisms by which these checkpoints work are largely unknown. PP2A associated with the Rts1 regulatory subunit (PP2A(Rts1)) is required for cell size control in budding yeast, but the relevant targets are unknown. In this paper, we used quantitative proteome-wide mass spectrometry to identify proteins controlled by PP2A(Rts1). This revealed that PP2A(Rts1) controls the two key checkpoint pathways thought to regulate the cell cycle in response to cell growth. To investigate the role of PP2A(Rts1) in these pathways, we focused on the Ace2 transcription factor, which is thought to delay cell cycle entry by repressing transcription of the G1 cyclin CLN3. Diverse experiments suggest that PP2A(Rts1) promotes cell cycle entry by inhibiting the repressor functions of Ace2. We hypothesize that control of Ace2 by PP2A(Rts1) plays a role in mechanisms that link G1 cyclin accumulation to cell growth.
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Affiliation(s)
- Jessica Zapata
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064
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39
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Abstract
The Hippo pathway controls metazoan organ growth by regulating cell proliferation and apoptosis. Many components have been identified, but our knowledge of the composition and structure of this pathway is still incomplete. Using existing pathway components as baits, we generated by mass spectrometry a high-confidence Drosophila Hippo protein-protein interaction network (Hippo-PPIN) consisting of 153 proteins and 204 interactions. Depletion of 67% of the proteins by RNA interference regulated the transcriptional coactivator Yorkie (Yki) either positively or negatively. We selected for further characterization a new member of the alpha-arrestin family, Leash, and show that it promotes degradation of Yki through the lysosomal pathway. Given the importance of the Hippo pathway in tumor development, the Hippo-PPIN will contribute to our understanding of this network in both normal growth and cancer.
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Affiliation(s)
- Young Kwon
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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40
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Abstract
A mechanistic understanding of signaling networks requires identification and analysis of phosphorylation sites. Mass spectrometry offers a rapid and highly sensitive approach to mapping phosphorylation sites. However, mass spectrometry has significant limitations that must be considered when planning to carry out phosphorylation-site mapping. Here we provide an overview of key information that should be taken into consideration before beginning phosphorylation-site analysis, as well as a step-by-step guide for carrying out successful experiments.
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Affiliation(s)
- Noah Dephoure
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115-5701, USA
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41
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Laurent G, German NJ, Saha AK, de Boer VCJ, Davies M, Koves TR, Dephoure N, Fischer F, Boanca G, Vaitheesvaran B, Lovitch SB, Sharpe AH, Kurland IJ, Steegborn C, Gygi SP, Muoio DM, Ruderman NB, Haigis MC. SIRT4 coordinates the balance between lipid synthesis and catabolism by repressing malonyl CoA decarboxylase. Mol Cell 2013; 50:686-98. [PMID: 23746352 DOI: 10.1016/j.molcel.2013.05.012] [Citation(s) in RCA: 262] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 03/22/2013] [Accepted: 05/02/2013] [Indexed: 12/01/2022]
Abstract
Lipid metabolism is tightly controlled by the nutritional state of the organism. Nutrient-rich conditions increase lipogenesis, whereas nutrient deprivation promotes fat oxidation. In this study, we identify the mitochondrial sirtuin, SIRT4, as a regulator of lipid homeostasis. SIRT4 is active in nutrient-replete conditions to repress fatty acid oxidation while promoting lipid anabolism. SIRT4 deacetylates and inhibits malonyl CoA decarboxylase (MCD), an enzyme that produces acetyl CoA from malonyl CoA. Malonyl CoA provides the carbon skeleton for lipogenesis and also inhibits fat oxidation. Mice lacking SIRT4 display elevated MCD activity and decreased malonyl CoA in skeletal muscle and white adipose tissue. Consequently, SIRT4 KO mice display deregulated lipid metabolism, leading to increased exercise tolerance and protection against diet-induced obesity. In sum, this work elucidates SIRT4 as an important regulator of lipid homeostasis, identifies MCD as a SIRT4 target, and deepens our understanding of the malonyl CoA regulatory axis.
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Affiliation(s)
- Gaëlle Laurent
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
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Abstract
Mitochondrial dysfunction is associated with the development of many age-related human diseases. Therefore recognizing and correcting the early signs of malfunctioning mitochondria is of critical importance for cellular welfare and survival. We previously demonstrated that VCP/Cdc48-associated mitochondrial stress responsive 1 (Vms1) is a component of a mitochondrial surveillance system that mediates the stress-responsive degradation of mitochondrial proteins by the proteasome. Here we propose novel mechanisms through which Vms1 monitors the status of mitochondria and is recruited to damaged or stressed mitochondria. We find that Vms1 contains a highly conserved region that is necessary and sufficient for mitochondrial targeting (the mitochondrial targeting domain [MTD]). Of interest, MTD-mediated mitochondrial targeting of Vms1 is negatively regulated by a direct interaction with the Vms1 N-terminus. Using laser-induced generation of mitochondrial reactive oxygen species, we also show that Vms1 is preferentially recruited to mitochondria subjected to oxidative stress. These studies define cellular and biochemical mechanisms by which Vms1 locali-zation to mitochondria is controlled to enable an efficient protein quality control system.
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Affiliation(s)
- Jin-Mi Heo
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
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43
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Laurent G, German NJ, Saha AK, de Boer VCJ, Fischer F, Boanca G, Dephoure N, Vaitheesvaran B, Davies M, Gygi SP, Muoio DM, Kurland IJ, Steegborn C, Ruderman NB, Haigis MC. SIRT4 controls the balance between lipid synthesis and catabolism by repressing malonyl-CoA decarboxylase. BMC Proc 2012. [PMCID: PMC3374230 DOI: 10.1186/1753-6561-6-s3-p30] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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44
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Bricker DK, Taylor EB, Schell JC, Orsak T, Boutron A, Chen YC, Cox JE, Cardon CM, Van Vranken JG, Dephoure N, Redin C, Boudina S, Gygi SP, Brivet M, Thummel CS, Rutter J. A mitochondrial pyruvate carrier required for pyruvate uptake in yeast, Drosophila, and humans. Science 2012; 337:96-100. [PMID: 22628558 DOI: 10.1126/science.1218099] [Citation(s) in RCA: 599] [Impact Index Per Article: 49.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Pyruvate constitutes a critical branch point in cellular carbon metabolism. We have identified two proteins, Mpc1 and Mpc2, as essential for mitochondrial pyruvate transport in yeast, Drosophila, and humans. Mpc1 and Mpc2 associate to form an ~150-kilodalton complex in the inner mitochondrial membrane. Yeast and Drosophila mutants lacking MPC1 display impaired pyruvate metabolism, with an accumulation of upstream metabolites and a depletion of tricarboxylic acid cycle intermediates. Loss of yeast Mpc1 results in defective mitochondrial pyruvate uptake, and silencing of MPC1 or MPC2 in mammalian cells impairs pyruvate oxidation. A point mutation in MPC1 provides resistance to a known inhibitor of the mitochondrial pyruvate carrier. Human genetic studies of three families with children suffering from lactic acidosis and hyperpyruvatemia revealed a causal locus that mapped to MPC1, changing single amino acids that are conserved throughout eukaryotes. These data demonstrate that Mpc1 and Mpc2 form an essential part of the mitochondrial pyruvate carrier.
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Affiliation(s)
- Daniel K Bricker
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
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45
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Dephoure N, Gygi SP. Hyperplexing: a method for higher-order multiplexed quantitative proteomics provides a map of the dynamic response to rapamycin in yeast. Sci Signal 2012; 5:rs2. [PMID: 22457332 DOI: 10.1126/scisignal.2002548] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Large-scale quantitative proteomics can provide a near-global view of cellular protein abundance. Yet, the time, effort, and expertise required to achieve reasonable protein coverage and reliable quantification have limited the broad application of this technology. To fully leverage mass spectrometry for the elucidation of biological systems requires sufficient throughput to monitor dynamic changes across conditions and to enable replicate analysis to provide statistical power. We report a straightforward approach to increase the multiplexing capacity of quantitative mass spectrometry, which provides a platform for the analysis of cellular signaling pathways. Using triplex metabolic labeling and six-plex isobaric tags, we monitored changes in protein abundance from 18 samples simultaneously, performing biological triplicates of a six-point time course of rapamycin-stimulated yeast. The data set provides temporal abundance profiles for thousands of yeast proteins, highlighting the complex cellular roles of the TOR (target of rapamycin) pathway.
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Affiliation(s)
- Noah Dephoure
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
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46
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Gygi SP, Huttlin EL, Wu R, Haas W, Dephoure N, Sowa M, Zhai B. Reply to "Phosphorylation sites of higher stoichiometry are more conserved". Nat Methods 2012. [DOI: 10.1038/nmeth.1942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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47
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Chen YC, Taylor EB, Dephoure N, Heo JM, Tonhato A, Papandreou I, Nath N, Denko NC, Gygi SP, Rutter J. Identification of a protein mediating respiratory supercomplex stability. Cell Metab 2012; 15:348-60. [PMID: 22405070 PMCID: PMC3302151 DOI: 10.1016/j.cmet.2012.02.006] [Citation(s) in RCA: 175] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 12/27/2011] [Accepted: 02/08/2012] [Indexed: 11/18/2022]
Abstract
The complexes of the electron transport chain associate into large macromolecular assemblies, which are believed to facilitate efficient electron flow. We have identified a conserved mitochondrial protein, named respiratory supercomplex factor 1 (Rcf1-Yml030w), that is required for the normal assembly of respiratory supercomplexes. We demonstrate that Rcf1 stably and independently associates with both Complex III and Complex IV of the electron transport chain. Deletion of the RCF1 gene caused impaired respiration, probably as a result of destabilization of respiratory supercomplexes. Consistent with the hypothetical function of these respiratory assemblies, loss of RCF1 caused elevated mitochondrial oxidative stress and damage. Finally, we show that knockdown of HIG2A, a mammalian homolog of RCF1, causes impaired supercomplex formation. We suggest that Rcf1 is a member of an evolutionarily conserved protein family that acts to promote respiratory supercomplex assembly and activity.
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Affiliation(s)
- Yu-Chan Chen
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
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48
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Harvey SL, Enciso G, Dephoure N, Gygi SP, Gunawardena J, Kellogg DR. A phosphatase threshold sets the level of Cdk1 activity in early mitosis in budding yeast. Mol Biol Cell 2011; 22:3595-608. [PMID: 21849476 PMCID: PMC3183015 DOI: 10.1091/mbc.e11-04-0340] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 08/01/2011] [Accepted: 08/08/2011] [Indexed: 01/07/2023] Open
Abstract
Entry into mitosis is initiated by synthesis of cyclins, which bind and activate cyclin-dependent kinase 1 (Cdk1). Cyclin synthesis is gradual, yet activation of Cdk1 occurs in a stepwise manner: a low level of Cdk1 activity is initially generated that triggers early mitotic events, which is followed by full activation of Cdk1. Little is known about how stepwise activation of Cdk1 is achieved. A key regulator of Cdk1 is the Wee1 kinase, which phosphorylates and inhibits Cdk1. Wee1 and Cdk1 show mutual regulation: Cdk1 phosphorylates Wee1, which activates Wee1 to inhibit Cdk1. Further phosphorylation events inactivate Wee1. We discovered that a specific form of protein phosphatase 2A (PP2A(Cdc55)) opposes the initial phosphorylation of Wee1 by Cdk1. In vivo analysis, in vitro reconstitution, and mathematical modeling suggest that PP2A(Cdc55) sets a threshold that limits activation of Wee1, thereby allowing a low constant level of Cdk1 activity to escape Wee1 inhibition in early mitosis. These results define a new role for PP2A(Cdc55) and reveal a systems-level mechanism by which dynamically opposed kinase and phosphatase activities can modulate signal strength.
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Affiliation(s)
- Stacy L. Harvey
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Germán Enciso
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Noah Dephoure
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | | | - Douglas R. Kellogg
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064
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Wu R, Dephoure N, Haas W, Huttlin EL, Zhai B, Sowa ME, Gygi SP. Correct interpretation of comprehensive phosphorylation dynamics requires normalization by protein expression changes. Mol Cell Proteomics 2011. [PMID: 21551504 DOI: 10.1074/mcp.m1111.009654] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
The interpretation of quantitative phosphoproteomics studies is complicated because each differential phosphorylation event integrates both changes in protein expression and phosphorylation. Here we investigated this phenomenon by performing parallel comparisons of protein expression and phosphorylation in S. cerevisiae. In each of two experiments comparing yeast mutants bearing deletions in FUS3 or STE7 with their wild-type counterparts, we quantified over 4100 proteins, including all members of the yeast mating pathway. We also identified 12,499 unique phosphorylation sites in this work. We demonstrate the critical importance of controlling the protein-level false-discovery rate and provide a novel method to assess the accuracy of protein false-discovery rate estimates. For the first time, 96% of nonredundant phosphopeptide ratios could be calibrated by protein levels, allowing truly differential phosphorylation to be distinguished from altered protein expression. This revealed a starkly different view, with 25% of seemingly differential phosphopeptides now attributed to changes in protein expression. Combined protein expression and phosphorylation surveys uncovered both independent and concerted changes in protein expression and phosphorylation, while highlighting the partially redundant role of a second MAPK (Kss1) in the mating pathway.
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Affiliation(s)
- Ronghu Wu
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
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50
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Wu R, Haas W, Dephoure N, Huttlin EL, Zhai B, Sowa ME, Gygi SP. A large-scale method to measure absolute protein phosphorylation stoichiometries. Nat Methods 2011; 8:677-83. [PMID: 21725298 PMCID: PMC3146562 DOI: 10.1038/nmeth.1636] [Citation(s) in RCA: 236] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 05/11/2011] [Indexed: 12/22/2022]
Abstract
The underlying functional role of protein phosphorylation is impacted by its fractional stoichiometry. Thus, a comprehensive strategy to study phosphorylation dynamics should include an assessment of site stoichiometry. Here, we developed an integrated method that relies on phosphatase treatment and stable isotope labeling to determine the absolute stoichiometries of protein phosphorylation on a large-scale. This approach requires the measurement of only a single ratio relating phosphatase- and mock-treated samples. We applied the strategy to determine stoichiometries for 5,033 phosphorylation sites in Saccharomyces cerevisiae. Stoichiometries were determined from biological triplicate experiments with good reproducibility. We validated ten sites stoichiometries representing the full range of values with an absolute quantitative approach, showing excellent agreement. Using bioinformatics, we characterized the biological properties associated with phosphorylation sites with vastly differing absolute stoichiometries.
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Affiliation(s)
- Ronghu Wu
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
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