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Gunasekharan V, Lin HK, Marczyk M, Rios-Hoyo A, Campos GE, Shan NL, Ahmed M, Umlauf S, Gareiss P, Raaisa R, Williams R, Cardone R, Siebel S, Kibbey R, Surovtseva YV, Pusztai L. Phosphoenolpyruvate carboxykinase-2 (PCK2) is a therapeutic target in triple-negative breast cancer. Breast Cancer Res Treat 2024; 208:657-671. [PMID: 39177932 DOI: 10.1007/s10549-024-07462-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 08/07/2024] [Indexed: 08/24/2024]
Abstract
PURPOSE Metabolic rewiring in malignant transformation is often accompanied by altered expression of metabolic isozymes. Phosphoenolpyruvate carboxykinase-2 (PCK2) catalyzes the rate-limiting step of gluconeogenesis and is the dominant isoform in many cancers including triple-negative breast cancer (TNBC). Our goal was to identify small molecule inhibitors of PCK2 enzyme activity. METHODS We assessed the impact of PCK2 down regulation with shRNA on TNBC cell growth in vitro and used AtomNet® deep convolutional neural network software to identify potential small molecule inhibitors of PCK2-based structure. We iteratively tested candidate compounds in an in vitro PCK-2 enzyme assay. The impact of the top hit on metabolic flux and cell viability was also assessed. RESULTS PCK2 downregulation decreased growth of BT-549 and MDA-MB-231 cells and reduced metabolic flux through pyruvate carboxylase. The first AtomNet® in silico structural screen of 7 million compounds yielded 86 structures that were tested in PCK2 enzyme assay in vitro. The top hit (IC50 = 2.4 µM) was used to refine a second round of in silico screen that yielded 82 candidates to be tested in vitro, which resulted in 45 molecules with inhibition > 20%. In the second in vitro screen we also included 3-(3,4-dihydroxyphenyl)-2-hydroxypropanoate, previously suggested to be PCK2 inhibitor based on structure, which emerged as the top hit. The specificity of this compound was tested in PCK1 and PCK2 enzymatic assays and showed IC50 of 500 nM and 3.5-27 nM for PCK1 and PCK2, respectively. CONCLUSION 3-(3,4-dihydroxyphenyl)-2-hydroxypropanoate is a high affinity PCK2 enzyme inhibitor that also has significant growth inhibitory activity in breast cell lines in vitro and represents a potential therapeutic lead compound.
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Affiliation(s)
- Vignesh Gunasekharan
- Yale Cancer Center, Yale School of Medicine, 300 George Street, Suite 120, Rm 133, New Haven, CT, 06511, USA
| | - Hao-Kuen Lin
- Yale Cancer Center, Yale School of Medicine, 300 George Street, Suite 120, Rm 133, New Haven, CT, 06511, USA
| | - Michal Marczyk
- Yale Cancer Center, Yale School of Medicine, 300 George Street, Suite 120, Rm 133, New Haven, CT, 06511, USA
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Alejandro Rios-Hoyo
- Yale Cancer Center, Yale School of Medicine, 300 George Street, Suite 120, Rm 133, New Haven, CT, 06511, USA
| | - Gerson Espinoza Campos
- Yale Cancer Center, Yale School of Medicine, 300 George Street, Suite 120, Rm 133, New Haven, CT, 06511, USA
| | - Naing Lin Shan
- Yale Cancer Center, Yale School of Medicine, 300 George Street, Suite 120, Rm 133, New Haven, CT, 06511, USA
| | | | - Sheila Umlauf
- Yale Center for Molecular Discovery, Yale University, West Haven, CT, USA
| | - Peter Gareiss
- Yale Center for Molecular Discovery, Yale University, West Haven, CT, USA
| | - Raaisa Raaisa
- Yale Cancer Center, Yale School of Medicine, 300 George Street, Suite 120, Rm 133, New Haven, CT, 06511, USA
| | - Richard Williams
- Yale Cancer Center, Yale School of Medicine, 300 George Street, Suite 120, Rm 133, New Haven, CT, 06511, USA
| | - Rebecca Cardone
- Yale Cancer Center, Yale School of Medicine, 300 George Street, Suite 120, Rm 133, New Haven, CT, 06511, USA
| | - Stephan Siebel
- Yale Cancer Center, Yale School of Medicine, 300 George Street, Suite 120, Rm 133, New Haven, CT, 06511, USA
| | - Richard Kibbey
- Yale Cancer Center, Yale School of Medicine, 300 George Street, Suite 120, Rm 133, New Haven, CT, 06511, USA
| | - Yulia V Surovtseva
- Yale Center for Molecular Discovery, Yale University, West Haven, CT, USA
| | - Lajos Pusztai
- Yale Cancer Center, Yale School of Medicine, 300 George Street, Suite 120, Rm 133, New Haven, CT, 06511, USA.
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Jiang P, Zhao S, Li X, Hu S, Chen S, Liang Y, Zhang L, Lu L, Fang G, Yang L, Huang Y, Miller H, Guan F, Lei J, Liu C. Dedicator of cytokinesis 8 (DOCK8) mutation impairs the differentiation of helper T cells by regulating the glycolytic pathway of CD4 + T cells. MedComm (Beijing) 2024; 5:e747. [PMID: 39329018 PMCID: PMC11424684 DOI: 10.1002/mco2.747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 08/28/2024] [Accepted: 08/29/2024] [Indexed: 09/28/2024] Open
Abstract
Dedicator of cytokinesis 8 (DOCK8) deficiency is a primary immunodeficiency disease caused by mutations in exon 45 of the DOCK8 gene. The clinical signs primarily consist of increased serum IgE levels, eczema, repeated skin infections, allergies, and upper respiratory tract infections. Using CRISPR/Cas9 technology, we generated a DOCK8 exon 45 mutation in mice, mirroring the mutation found in patients. The results indicated that DOCK8 mutation impairs peripheral T cell homeostasis, disrupts regulatory T cells (Tregs) development, increases ICOS expression in Tregs within peripheral lymph nodes (pLn), and promotes Th17 cell differentiation within the spleen and pLn. Upon virus infection, DOCK8 mutation CD4+ T cells have a Th2 effector fate. RNA-bulk sequencing data revealed alternations in the mTOR pathway of DOCK8 mutant CD4+ T cells. We observed that DOCK8 mutation upregulates the glycolysis levels in CD4+ T cells, which is related to the Akt/mTOR/S6/HIF-1α pathway. In summary, our research elucidates that DOCK8 regulates the differentiation of helper T cells by modulating the glycolytic pathway in CD4+ T cells, thereby advancing the comprehension and offering potential treatment of diseases in DOCK8-deficient patients.
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Affiliation(s)
- Panpan Jiang
- Department of Pathogen Biology School of Basic Medicine Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases Huazhong University of Science and Technology Wuhan China
| | - Siyu Zhao
- Department Immunology School of Medicine Yangtze University Jingzhou China
| | - Xiaoyu Li
- Department of Pathogen Biology School of Basic Medicine Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases Huazhong University of Science and Technology Wuhan China
| | - Shiyan Hu
- Department of Pathogen Biology School of Basic Medicine Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases Huazhong University of Science and Technology Wuhan China
| | - Shuhan Chen
- Department of Pathogen Biology School of Basic Medicine Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases Huazhong University of Science and Technology Wuhan China
| | - Yinming Liang
- Center of Disease Model and Immunology Hunan Academy of Chinese Medicine Changsha China
| | - Lichen Zhang
- Laboratory of Genetic Regulators in the Immune System School of Medical Technology Xinxiang Medical University Xinxiang China
| | - Liaoxun Lu
- Laboratory of Genetic Regulators in the Immune System School of Medical Technology Xinxiang Medical University Xinxiang China
| | - Guofeng Fang
- Department of Pathogen Biology School of Basic Medicine Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases Huazhong University of Science and Technology Wuhan China
| | - Lu Yang
- Department of Pathogen Biology School of Basic Medicine Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases Huazhong University of Science and Technology Wuhan China
| | - Yanmei Huang
- Department of Pathogen Biology School of Basic Medicine Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases Huazhong University of Science and Technology Wuhan China
| | - Heather Miller
- Cytek Biosciences R&D Clinical Reagents Fremont California USA
| | - Fei Guan
- Department of Pathogen Biology School of Basic Medicine Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases Huazhong University of Science and Technology Wuhan China
| | - Jiahui Lei
- Department of Pathogen Biology School of Basic Medicine Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases Huazhong University of Science and Technology Wuhan China
| | - Chaohong Liu
- Department of Pathogen Biology School of Basic Medicine Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases Huazhong University of Science and Technology Wuhan China
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Marczyk M, Gunasekharan V, Casadevall D, Qing T, Foldi J, Sehgal R, Shan NL, Blenman KRM, O'Meara TA, Umlauf S, Surovtseva YV, Muthusamy V, Rinehart J, Perry RJ, Kibbey R, Hatzis C, Pusztai L. Comprehensive Analysis of Metabolic Isozyme Targets in Cancer. Cancer Res 2022; 82:1698-1711. [PMID: 35247885 PMCID: PMC10883296 DOI: 10.1158/0008-5472.can-21-3983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/07/2022] [Accepted: 02/21/2022] [Indexed: 11/16/2022]
Abstract
Metabolic reprogramming is a hallmark of malignant transformation, and loss of isozyme diversity (LID) contributes to this process. Isozymes are distinct proteins that catalyze the same enzymatic reaction but can have different kinetic characteristics, subcellular localization, and tissue specificity. Cancer-dominant isozymes that catalyze rate-limiting reactions in critical metabolic processes represent potential therapeutic targets. Here, we examined the isozyme expression patterns of 1,319 enzymatic reactions in 14 cancer types and their matching normal tissues using The Cancer Genome Atlas mRNA expression data to identify isozymes that become cancer-dominant. Of the reactions analyzed, 357 demonstrated LID in at least one cancer type. Assessment of the expression patterns in over 600 cell lines in the Cancer Cell Line Encyclopedia showed that these reactions reflect cellular changes instead of differences in tissue composition; 50% of the LID-affected isozymes showed cancer-dominant expression in the corresponding cell lines. The functional importance of the cancer-dominant isozymes was assessed in genome-wide CRISPR and RNAi loss-of-function screens: 17% were critical for cell proliferation, indicating their potential as therapeutic targets. Lists of prioritized novel metabolic targets were developed for 14 cancer types; the most broadly shared and functionally validated target was acetyl-CoA carboxylase 1 (ACC1). Small molecule inhibition of ACC reduced breast cancer viability in vitro and suppressed tumor growth in cell line- and patient-derived xenografts in vivo. Evaluation of the effects of drug treatment revealed significant metabolic and transcriptional perturbations. Overall, this systematic analysis of isozyme expression patterns elucidates an important aspect of cancer metabolic plasticity and reveals putative metabolic vulnerabilities. SIGNIFICANCE This study exploits the loss of metabolic isozyme diversity common in cancer and reveals a rich pool of potential therapeutic targets that will allow the repurposing of existing inhibitors for anticancer therapy. See related commentary by Kehinde and Parker, p. 1695.
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Affiliation(s)
- Michal Marczyk
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
| | | | - David Casadevall
- Cancer Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain
| | - Tao Qing
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Julia Foldi
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Raghav Sehgal
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Naing Lin Shan
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Kim R M Blenman
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Tess A O'Meara
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Sheila Umlauf
- Yale Center for Molecular Discovery, Yale University, West Haven, Connecticut
| | - Yulia V Surovtseva
- Yale Center for Molecular Discovery, Yale University, West Haven, Connecticut
| | - Viswanathan Muthusamy
- Center for Precision Cancer Modeling, Yale School of Medicine, New Haven, Connecticut
| | - Jesse Rinehart
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Rachel J Perry
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Richard Kibbey
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Christos Hatzis
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Lajos Pusztai
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
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Chen CY, Chen J, He L, Stiles BL. PTEN: Tumor Suppressor and Metabolic Regulator. Front Endocrinol (Lausanne) 2018; 9:338. [PMID: 30038596 PMCID: PMC6046409 DOI: 10.3389/fendo.2018.00338] [Citation(s) in RCA: 376] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/05/2018] [Indexed: 12/19/2022] Open
Abstract
Phosphatase and Tensin Homolog deleted on Chromosome 10 (PTEN) is a dual phosphatase with both protein and lipid phosphatase activities. PTEN was first discovered as a tumor suppressor with growth and survival regulatory functions. In recent years, the function of PTEN as a metabolic regulator has attracted significant attention. As the lipid phosphatase that dephosphorylates phosphatidylinositol-3, 4, 5-phosphate (PIP3), PTEN reduces the level of PIP3, a critical 2nd messenger mediating the signal of not only growth factors but also insulin. In this review, we introduced the discovery of PTEN, the PTEN-regulated canonical and nuclear signals, and PTEN regulation. We then focused on the role of PTEN and PTEN-regulated signals in metabolic regulation. This included the role of PTEN in glycolysis, gluconeogenesis, glycogen synthesis, lipid metabolism as well as mitochondrial metabolism. We also included how PTEN and PTEN regulated metabolic functions may act paradoxically toward insulin sensitivity and tumor metabolism and growth. Further understanding of how PTEN regulates metabolism and how such regulations lead to different biological outcomes is necessary for interventions targeting at the PTEN-regulated signals in either cancer or diabetes treatment.
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Affiliation(s)
- Chien-Yu Chen
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Jingyu Chen
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Lina He
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Bangyan L. Stiles
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- *Correspondence: Bangyan L. Stiles
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Bipartite network analysis reveals metabolic gene expression profiles that are highly associated with the clinical outcomes of acute myeloid leukemia. Comput Biol Chem 2017; 67:150-157. [DOI: 10.1016/j.compbiolchem.2017.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 11/30/2016] [Accepted: 01/05/2017] [Indexed: 02/08/2023]
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