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Jenkins EC, Casalena G, Gomez M, Zhao D, Kenny TC, Shah N, Manfredi G, Germain D. Raloxifene is a Female-specific Proteostasis Therapeutic in the Spinal Cord. Endocrinology 2021; 162:6017493. [PMID: 33269387 PMCID: PMC7774777 DOI: 10.1210/endocr/bqaa221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Indexed: 02/06/2023]
Abstract
Several neurodegenerative disorders are characterized by proteasome dysfunctions leading to protein aggregations and pathogenesis. Since we showed that estrogen receptor alpha (ERα) activates the proteasome, drugs able to stimulate ERα in the central nervous system (CNS) could hold potential for therapeutic intervention. However, the transcriptional effects of selective estrogen receptor modulators (SERMs), such as tamoxifen and raloxifene, can be tissue specific. A direct comparison of the effects of different SERMs on gene transcription in the CNS has never been performed. Here, we report an RNA-seq analysis of the spinal cord treated with estrogen, tamoxifen, or raloxifene. We find stark SERM and sex-specific differences in gene expression profiles in the spinal cord. Notably, raloxifene, but not estrogen or tamoxifen, modulates numerous deubiquitinating enzymes, proteasome subunits and assembly factors, and these effects translate into decreased protein aggregates. In the SOD1-G93A mouse model of amyotrophic lateral sclerosis, we found that even a low dose of raloxifene causes a significant decrease in mutant SOD1 aggregates in the spinal cord, accompanied by a delay in the decline of muscle strength in females, but not in males. These results strongly indicate SERM-selective as well as sex-specific effects, and emphasize the importance of sex as a biological variable to be considered for the careful selection of specific SERM for use in clinical trials for neurodegenerative diseases.
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Affiliation(s)
- Edmund Charles Jenkins
- Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, Department of Medicine, Division of Hematology/Oncology, New York, NY, USA
| | - Gabriella Casalena
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Maria Gomez
- Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, Department of Medicine, Division of Hematology/Oncology, New York, NY, USA
| | - Dazhi Zhao
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Timothy C Kenny
- Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, Department of Medicine, Division of Hematology/Oncology, New York, NY, USA
| | - Nagma Shah
- Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, Department of Medicine, Division of Hematology/Oncology, New York, NY, USA
| | - Giovanni Manfredi
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Correspondence: Doris Germain, Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, Department of Medicine, Division of Hematology/Oncology, New York, 10029 NY, USA. ; or Giovanni Manfredi, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, 10065 NY, USA.
| | - Doris Germain
- Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, Department of Medicine, Division of Hematology/Oncology, New York, NY, USA
- Correspondence: Doris Germain, Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, Department of Medicine, Division of Hematology/Oncology, New York, 10029 NY, USA. ; or Giovanni Manfredi, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, 10065 NY, USA.
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Estrogen and estrogen receptors chauffeur the sex-biased autophagic action in liver. Cell Death Differ 2020; 27:3117-3130. [PMID: 32483382 DOI: 10.1038/s41418-020-0567-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 05/20/2020] [Accepted: 05/20/2020] [Indexed: 01/02/2023] Open
Abstract
Autophagy, or cellular self-digestion, is an essential cellular process imperative for energy homeostasis, development, differentiation, and survival. However, the intrinsic factors that bring about the sex-biased differences in liver autophagy are still unknown. In this work, we found that autophagic genes variably expresses in the steroidogenic tissues, mostly abundant in liver, and is influenced by the individual's sexuality. Starvation-induced autophagy in a time-dependent female-dominated manner, and upon starvation, a strong gender responsive circulating steroid-HK2 relation was observed, which highlighted the importance of estrogen in autophagy regulation. This was further confirmed by the enhanced or suppressed autophagy upon estrogen addition (male) or blockage (female), respectively. In addition, we found that estrogen proved to be the common denominator between stress management, glucose metabolism, and autophagic action in female fish. To understand further, we used estrogen receptor (ER)α- and ER-β2-knockout (KO) medaka and found ER-specific differences in sex-biased autophagy. Interestingly, starvation resulted in significantly elevated mTOR transcription (compared with control) in male ERα-KO fish while HK2 and ULK activation was greatly decreased in both KO fish in a female oriented fashion. Later, ChIP analysis confirmed that, NRF2, an upstream regulator of mTOR, only binds to ERα, while both ERα and ERβ2 are effectively pulled down the HK2 and LC3. FIHC data show that, in both ER-KO fish, LC3 nuclear-cytoplasmic transport and its associated pathways involving SIRT1 and DOR were greatly affected. Cumulatively, our data suggest that, ERα-KO strongly affected the early autophagic initiation and altered the LC3 nuclear-cytoplasmic translocation, thereby influencing the sex-biased final autophagosome formation in medaka. Thus, existence of steroid responsive autophagy regulatory-switches and sex-biased steroid/steroid receptor availability influences the gender-skewed autophagy. Expectedly, this study may furnish newer appreciation for gender-specific medicine research and therapeutics.
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Zhu Y, Zou X, Dean AE, Brien JO, Gao Y, Tran EL, Park SH, Liu G, Kieffer MB, Jiang H, Stauffer ME, Hart R, Quan S, Satchell KJF, Horikoshi N, Bonini M, Gius D. Lysine 68 acetylation directs MnSOD as a tetrameric detoxification complex versus a monomeric tumor promoter. Nat Commun 2019; 10:2399. [PMID: 31160585 PMCID: PMC6546705 DOI: 10.1038/s41467-019-10352-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 04/29/2019] [Indexed: 12/12/2022] Open
Abstract
Manganese superoxide dismutase (MnSOD) functions as a tumor suppressor; however, once tumorigenesis occurs, clinical data suggest MnSOD levels correlate with more aggressive human tumors, implying a potential dual function of MnSOD in the regulation of metabolism. Here we show, using in vitro transformation and xenograft growth assays that the MnSOD-K68 acetylation (Ac) mimic mutant (MnSODK68Q) functions as a tumor promoter. Interestingly, in various breast cancer and primary cell types the expression of MnSODK68Q is accompanied with a change of MnSOD's stoichiometry from a known homotetramer complex to a monomeric form. Biochemical experiments using the MnSOD-K68Q Ac-mimic, or physically K68-Ac (MnSOD-K68-Ac), suggest that these monomers function as a peroxidase, distinct from the established MnSOD superoxide dismutase activity. MnSODK68Q expressing cells exhibit resistance to tamoxifen (Tam) and cells selected for Tam resistance exhibited increased K68-Ac and monomeric MnSOD. These results suggest a MnSOD-K68-Ac metabolic pathway for Tam resistance, carcinogenesis and tumor progression.
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Affiliation(s)
- Yueming Zhu
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Xianghui Zou
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Driskill Graduate Program in Life Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Angela E Dean
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Joseph O' Brien
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Yucheng Gao
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Driskill Graduate Program in Life Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Elizabeth L Tran
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Seong-Hoon Park
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
- Department of General and Applied Toxicology, Innovative Toxicology Research Center, Korea Institute of Toxicology (KIT), Daejeon, 34114, Korea
| | - Guoxiang Liu
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Matthew B Kieffer
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Haiyan Jiang
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | | | - Robert Hart
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Songhua Quan
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Karla J F Satchell
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Nobuo Horikoshi
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Marcelo Bonini
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - David Gius
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
- Driskill Graduate Program in Life Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
- Department of Pharmacology, Robert H. Lurie Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
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Kong Y, Yu T. A graph-embedded deep feedforward network for disease outcome classification and feature selection using gene expression data. Bioinformatics 2018; 34:3727-3737. [PMID: 29850911 PMCID: PMC6198851 DOI: 10.1093/bioinformatics/bty429] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/30/2018] [Accepted: 05/23/2018] [Indexed: 12/16/2022] Open
Abstract
Motivation Gene expression data represents a unique challenge in predictive model building, because of the small number of samples (n) compared with the huge amount of features (p). This 'n≪p' property has hampered application of deep learning techniques for disease outcome classification. Sparse learning by incorporating external gene network information could be a potential solution to this issue. Still, the problem is very challenging because (i) there are tens of thousands of features and only hundreds of training samples, (ii) the scale-free structure of the gene network is unfriendly to the setup of convolutional neural networks. Results To address these issues and build a robust classification model, we propose the Graph-Embedded Deep Feedforward Networks (GEDFN), to integrate external relational information of features into the deep neural network architecture. The method is able to achieve sparse connection between network layers to prevent overfitting. To validate the method's capability, we conducted both simulation experiments and real data analysis using a breast invasive carcinoma RNA-seq dataset and a kidney renal clear cell carcinoma RNA-seq dataset from The Cancer Genome Atlas. The resulting high classification accuracy and easily interpretable feature selection results suggest the method is a useful addition to the current graph-guided classification models and feature selection procedures. Availability and implementation The method is available at https://github.com/yunchuankong/GEDFN. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yunchuan Kong
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, USA
| | - Tianwei Yu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, USA
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Abstract
Macroautophagy/autophagy is vital for intracellular quality control and homeostasis. Therefore, careful regulation of autophagy is very important. In the past 10 years, a number of studies have reported that estrogenic effectors affect autophagy. However, some results, especially those regarding the modulatory effect of 17β-estradiol (E2) on autophagy seem inconsistent. Moreover, several clinical trials are already in place combining both autophagy inducers and autophagy inhibitors with endocrine therapies for breast cancer. Not all patients experience benefit, which further confuses and complicates our understanding of the main effects of autophagy in estrogen-related cancer. In view of the importance of the crosstalk between estrogen signaling and autophagy, this review summarizes the estrogenic effectors reported to affect autophagy, subcellular distribution and translocation of estrogen receptors, autophagy-targeted transcription factors (TFs), miRNAs, and histone modifications regulated by E2. Upon stimulation with estrogen, there will always be opposing functional actions, which might occur between different receptors, receptors on TFs, TFs on autophagy genes, or even histone modifications on transcription. The huge signaling network downstream of estrogen can promote autophagy and reduce overstimulated autophagy at the same time, which allows autophagy to be regulated by estrogen in a restricted range. To help understand how the estrogenic regulation of autophagy affects cell fate, a hypothetical model is presented here. Finally, we discuss some exciting new directions in the field. We hope this might help to better understand the multiple associations between estrogen and autophagy, the pathogenic mechanisms of many estrogen-related diseases, and to design novel and efficacious therapeutics. Abbreviations: AP-1, activator protein-1; HATs, histone acetyltransferases; HDAC, histone deacetylases; HOTAIR, HOX transcript antisense RNA.
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Affiliation(s)
- Jin Xiang
- a Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences , Wuhan University , Wuhan , PR China
| | - Xiang Liu
- a Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences , Wuhan University , Wuhan , PR China
| | - Jing Ren
- a Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences , Wuhan University , Wuhan , PR China
| | - Kun Chen
- a Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences , Wuhan University , Wuhan , PR China
| | - Hong-Lu Wang
- a Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences , Wuhan University , Wuhan , PR China
| | - Yu-Yang Miao
- a Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences , Wuhan University , Wuhan , PR China
| | - Miao-Miao Qi
- a Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences , Wuhan University , Wuhan , PR China
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Cook KL, Soto-Pantoja DR, Clarke PAG, Cruz MI, Zwart A, Wärri A, Hilakivi-Clarke L, Roberts DD, Clarke R. Endoplasmic Reticulum Stress Protein GRP78 Modulates Lipid Metabolism to Control Drug Sensitivity and Antitumor Immunity in Breast Cancer. Cancer Res 2016; 76:5657-5670. [PMID: 27698188 PMCID: PMC5117832 DOI: 10.1158/0008-5472.can-15-2616] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 06/03/2016] [Indexed: 02/07/2023]
Abstract
The unfolded protein response is an endoplasmic reticulum stress pathway mediated by the protein chaperone glucose regulated-protein 78 (GRP78). Metabolic analysis of breast cancer cells shows that GRP78 silencing increases the intracellular concentrations of essential polyunsaturated fats, including linoleic acid. Accumulation of fatty acids is due to an inhibition of mitochondrial fatty acid transport, resulting in a reduction of fatty acid oxidation. These data suggest a novel role of GRP78-mediating cellular metabolism. We validated the effect of GRP78-regulated metabolite changes by treating tumor-bearing mice with tamoxifen and/or linoleic acid. Tumors treated with linoleic acid plus tamoxifen exhibited reduced tumor area and tumor weight. Inhibition of either GRP78 or linoleic acid treatment increased MCP-1 serum levels, decreased CD47 expression, and increased macrophage infiltration, suggesting a novel role for GRP78 in regulating innate immunity. GRP78 control of fatty acid oxidation may represent a new homeostatic function for GRP78. Cancer Res; 76(19); 5657-70. ©2016 AACR.
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Affiliation(s)
- Katherine L Cook
- Department of Surgery and Hypertension and Vascular Research Center, Wake Forest University School of Medicine, Winston-Salem, North Carolina. Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC.
| | - David R Soto-Pantoja
- Department of Surgery and Hypertension and Vascular Research Center, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Pamela A G Clarke
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
| | - M Idalia Cruz
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
| | - Alan Zwart
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
| | - Anni Wärri
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
| | - Leena Hilakivi-Clarke
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
| | - David D Roberts
- Laboratory of Pathology, National Cancer Institute, NIH, Bethesda, Maryland
| | - Robert Clarke
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
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Clarke R, Cook KL. Unfolding the Role of Stress Response Signaling in Endocrine Resistant Breast Cancers. Front Oncol 2015; 5:140. [PMID: 26157705 PMCID: PMC4475795 DOI: 10.3389/fonc.2015.00140] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Accepted: 06/03/2015] [Indexed: 11/24/2022] Open
Abstract
The unfolded protein response (UPR) is an ancient stress response that enables a cell to manage the energetic stress that accompanies protein folding. There has been a significant recent increase in our understanding of the UPR, how it integrates physiological processes within cells, and how this integration can affect cancer cells and cell fate decisions. Recent publications have highlighted the role of UPR signaling components on mediating various cell survival pathways, cellular metabolism and bioenergenics, and autophagy. We address the role of UPR on mediating endocrine therapy resistance and estrogen receptor-positive breast cancer cell survival.
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Affiliation(s)
- Robert Clarke
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center , Washington, DC , USA
| | - Katherine L Cook
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center , Washington, DC , USA
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