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Lee DH, Yoo JK, Um KH, Ha W, Lee SM, Park J, Kye MJ, Suh J, Choi JW. Intravesical instillation-based mTOR-STAT3 dual targeting for bladder cancer treatment. J Exp Clin Cancer Res 2024; 43:170. [PMID: 38886756 PMCID: PMC11184849 DOI: 10.1186/s13046-024-03088-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 06/05/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Recent intravesical administration of adenoviral vectors, either as a single injection or in combination with immune checkpoint inhibitors, exemplified by cretostimogene grenadenorepvec and nadofaragene firadenovec, has demonstrated remarkable efficacy in clinical trials for non-muscle invasive bladder cancer. Despite their ability to induce an enhanced immune reaction within the lesion, the intracellular survival signaling of cancer cells has not been thoroughly addressed. METHODS An analysis of the prognostic data revealed a high probability of therapeutic efficacy with simultaneous inhibition of mTOR and STAT3. Considering the challenges of limited pharmaco-accessibility to the bladder due to its pathophysiological structure and the partially undruggable nature of target molecules, we designed a dual siRNA system targeting both mRNAs. Subsequently, this dual siRNA system was encoded into the adenovirus 5/3 (Ad 5/3) to enhance in vivo delivery efficiency. RESULTS Gene-targeting efficacy was assessed using cells isolated from xenografted tumors using a single-cell analysis system. Our strategy demonstrated a balanced downregulation of mTOR and STAT3 at the single-cell resolution, both in vitro and in vivo. This approach reduced tumor growth in bladder cancer xenograft and orthotopic animal experiments. In addition, increased infiltration of CD8+ T cells was observed in a humanized mouse model. We provided helpful and safe tissue distribution data for intravesical therapy of siRNAs coding adenoviruses. CONCLUSIONS The bi-specific siRNA strategy, encapsulated in an adenovirus, could be a promising tool to augment cancer treatment efficacy and overcome conventional therapy limitations associated with "undruggability." Hence, we propose that dual targeting of mTOR and STAT3 is an advantageous strategy for intravesical therapy using adenoviruses.
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Affiliation(s)
- Dae Hoon Lee
- Department of Pharmacology, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea
- R&D Center of Curigin Ltd., Curigin, Seoul, 04778, Republic of Korea
| | - Jung Ki Yoo
- Department of Pharmacology, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea
- R&D Center of Curigin Ltd., Curigin, Seoul, 04778, Republic of Korea
| | - Ki Hwan Um
- Department of Pharmacology, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea
- R&D Center of Curigin Ltd., Curigin, Seoul, 04778, Republic of Korea
- Department of Regulatory Science, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Wootae Ha
- R&D Center of Curigin Ltd., Curigin, Seoul, 04778, Republic of Korea
| | - Soo Min Lee
- Department of Pharmacology, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea
- Department of Regulatory Science, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Junseong Park
- Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Min Jeong Kye
- R&D Center of Curigin Ltd., Curigin, Seoul, 04778, Republic of Korea
| | - Jungyo Suh
- Department of Urology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Jin Woo Choi
- Department of Pharmacology, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea.
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea.
- R&D Center of Curigin Ltd., Curigin, Seoul, 04778, Republic of Korea.
- Department of Regulatory Science, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea.
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2
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Srkalovic G, Nijim S, Srkalovic MB, Fajgenbaum D. Increase in Vascular Endothelial Growth Factor (VEGF) Expression and the Pathogenesis of iMCD-TAFRO. Biomedicines 2024; 12:1328. [PMID: 38927535 PMCID: PMC11201201 DOI: 10.3390/biomedicines12061328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/31/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
TAFRO (thrombocytopenia (T), anasarca (A), fever (F), reticulin fibrosis (F/R), renal failure (R), and organomegaly (O)) is a heterogeneous clinical subtype of idiopathic multicentric Castleman disease (iMCD) associated with a significantly poorer prognosis than other subtypes of iMCD. TAFRO symptomatology can also be seen in pathological contexts outside of iMCD, but it is unclear if those cases should be considered representative of a different disease entity or simply a severe presentation of other infectious, malignant, and rheumatological diseases. While interleukin-6 (IL-6) is an established driver of iMCD-TAFRO pathogenesis in a subset of patients, the etiology is unknown. Recent case reports and literature reviews on TAFRO patients suggest that vascular endothelial growth factor (VEGF), and the interplay of VEGF and IL-6 in concert, rather than IL-6 as a single cytokine, may be drivers for iMCD-TAFRO pathophysiology, especially renal injury. In this review, we discuss the possible role of VEGF in the pathophysiology and clinical manifestations of iMCD-TAFRO. In particular, VEGF may be involved in iMCD-TAFRO pathology through its ability to activate RAS/RAF/MEK/ERK and PI3K/AKT/mTOR signaling pathways. Further elucidating a role for the VEGF-IL-6 axis and additional disease drivers may shed light on therapeutic options for the treatment of TAFRO patients who do not respond to, or otherwise relapse following, treatment with IL-6 targeting drugs. This review investigates the potential role of VEGF in the pathophysiology of iMCD-TAFRO and the potential for targeting related signaling pathways in the future.
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Affiliation(s)
- Gordan Srkalovic
- Herbert-Herman Cancer Center, University of Michigan Health-Sparrow, Lansing, MI 48912, USA
| | - Sally Nijim
- Center for Cytokine Storm Treatment & Laboratory, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (S.N.); (D.F.)
| | | | - David Fajgenbaum
- Center for Cytokine Storm Treatment & Laboratory, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (S.N.); (D.F.)
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Zhang S, Cheng Y, Guan Y, Wen J, Chen Z. Hydrogen Sulfide Exerted a Pro-Angiogenic Role by Promoting the Phosphorylation of VEGFR2 at Tyr797 and Ser799 Sites in Hypoxia-Reoxygenation Injury. Int J Mol Sci 2024; 25:4340. [PMID: 38673925 PMCID: PMC11050214 DOI: 10.3390/ijms25084340] [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: 03/05/2024] [Revised: 03/25/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
The protective effects of hydrogen sulfide (H2S) against ischemic brain injury and its role in promoting angiogenesis have been established. However, the specific mechanism underlying these effects remains unclear. This study is designed to investigate the regulatory impact and mechanism of H2S on VEGFR2 phosphorylation. Following expression and purification, the recombinant His-VEGFR2 protein was subjected to LC-PRM/MS analysis to identify the phosphorylation sites of VEGFR2 upon NaHS treatment. Adenovirus infection was used to transfect primary rat brain artery endothelial cells (BAECs) with the Ad-VEGFR2WT, Ad-VEGFR2Y797F, and Ad-VEGFR2S799A plasmids. The expression of VEGFR2 and recombinant Flag-VEGFR2, along with Akt phosphorylation, cell proliferation, and LDH levels, was assessed. The migratory capacity and tube-forming potential of BAECs were assessed using wound healing, transwell, and tube formation assays. NaHS notably enhanced the phosphorylation of VEGFR2 at Tyr797 and Ser799 sites. These phosphorylation sites were identified as crucial for mediating the protective effects of NaHS against hypoxia-reoxygenation (H/R) injury. NaHS significantly enhanced the Akt phosphorylation, migratory capacity, and tube formation of BAECs and upregulated the expression of VEGFR2 and recombinant proteins. These findings suggest that Tyr797 and Ser799 sites of VEGFR2 serve as crucial mediators of H2S-induced pro-angiogenic effects and protection against H/R injury.
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Affiliation(s)
- Sen Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China; (S.Z.); (Y.G.)
| | - Yongfeng Cheng
- Clinical Medical College, Anhui Medical University, Hefei 230012, China;
| | - Yining Guan
- Department of Pharmacology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China; (S.Z.); (Y.G.)
| | - Jiyue Wen
- Department of Pharmacology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China; (S.Z.); (Y.G.)
| | - Zhiwu Chen
- Department of Pharmacology, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China; (S.Z.); (Y.G.)
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4
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Miyamura Y, Kamei S, Matsuo M, Yamazaki M, Usuki S, Yasunaga K, Uemura A, Satou Y, Ohguchi H, Minami T. FOXO1 stimulates tip cell-enriched gene expression in endothelial cells. iScience 2024; 27:109161. [PMID: 38444610 PMCID: PMC10914484 DOI: 10.1016/j.isci.2024.109161] [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: 01/05/2023] [Revised: 11/29/2023] [Accepted: 02/05/2024] [Indexed: 03/07/2024] Open
Abstract
Forkhead box O (FOXO) family proteins are expressed in various cells, and play crucial roles in cellular metabolism, apoptosis, and aging. FOXO1-null mice exhibit embryonic lethality due to impaired endothelial cell (EC) maturation and vascular remodeling. However, FOXO1-mediated genome-wide regulation in ECs remains unclear. Here, we demonstrate that VEGF dynamically regulates FOXO1 cytosol-nucleus translocation. FOXO1 re-localizes to the nucleus via PP2A phosphatase. RNA-seq combined with FOXO1 overexpression/knockdown in ECs demonstrated that FOXO1 governs the VEGF-responsive tip cell-enriched genes, and further inhibits DLL4-NOTCH signaling. Endogenous FOXO1 ChIP-seq revealed that FOXO1 binds to the EC-unique tip-enriched genes with co-enrichment of EC master regulators, and the condensed chromatin region as a pioneer factor. We identified new promoter/enhancer regions of the VEGF-responsive tip cell genes regulated by FOXO1: ESM1 and ANGPT2. This is the first study to identify cell type-specific FOXO1 functions, including VEGF-mediated tip cell definition in primary cultured ECs.
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Affiliation(s)
- Yuri Miyamura
- Divison of Molecular and Vascular Biology, IRDA, Kumamoto University, Kumamoto 860-0811, Japan
| | - Shunsuke Kamei
- Divison of Molecular and Vascular Biology, IRDA, Kumamoto University, Kumamoto 860-0811, Japan
| | - Misaki Matsuo
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-8556, Japan
| | - Masaya Yamazaki
- Division of Medical Biochemistry, Graduate School of Medical Science, Kumamoto University, Kumamoto 860-8556, Japan
| | - Shingo Usuki
- Liaison Laboratory Research Promotion Center, IMEG, Kumamoto University, Kumamoto 860-8556, Japan
| | - Keiichiro Yasunaga
- Liaison Laboratory Research Promotion Center, IMEG, Kumamoto University, Kumamoto 860-8556, Japan
| | - Akiyoshi Uemura
- Department of Retinal Vascular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan
| | - Yorifumi Satou
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-8556, Japan
| | - Hiroto Ohguchi
- Division of Disease Epigenetics, IRDA, Kumamoto University, Kumamoto 860-0811, Japan
| | - Takashi Minami
- Divison of Molecular and Vascular Biology, IRDA, Kumamoto University, Kumamoto 860-0811, Japan
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5
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Dominguez SL, Laufer BI, Ghosh AS, Li Q, Ruggeri G, Emani MR, Phu L, Friedman BA, Sandoval W, Rose CM, Ngu H, Foreman O, Reichelt M, Juste Y, Lalehzadeh G, Hansen D, Nymark H, Mellal D, Gylling H, Kiełpiński ŁJ, Chih B, Bingol B, Hoogenraad CC, Meilandt WJ, Easton A. TMEM106B reduction does not rescue GRN deficiency in iPSC-derived human microglia and mouse models. iScience 2023; 26:108362. [PMID: 37965143 PMCID: PMC10641752 DOI: 10.1016/j.isci.2023.108362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/28/2023] [Accepted: 10/25/2023] [Indexed: 11/16/2023] Open
Abstract
Heterozygous mutations in the granulin (GRN) gene are a leading cause of frontotemporal lobar degeneration with TDP-43 aggregates (FTLD-TDP). Polymorphisms in TMEM106B have been associated with disease risk in GRN mutation carriers and protective TMEM106B variants associated with reduced levels of TMEM106B, suggesting that lowering TMEM106B might be therapeutic in the context of FTLD. Here, we tested the impact of full deletion and partial reduction of TMEM106B in mouse and iPSC-derived human cell models of GRN deficiency. TMEM106B deletion did not reverse transcriptomic or proteomic profiles in GRN-deficient microglia, with a few exceptions in immune signaling markers. Neither homozygous nor heterozygous Tmem106b deletion normalized disease-associated phenotypes in Grn -/-mice. Furthermore, Tmem106b reduction by antisense oligonucleotide (ASO) was poorly tolerated in Grn -/-mice. These data provide novel insight into TMEM106B and GRN function in microglia cells but do not support lowering TMEM106B levels as a viable therapeutic strategy for treating FTD-GRN.
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Affiliation(s)
- Sara L. Dominguez
- Department of Neuroscience, Genentech, South San Francisco, CA 94080, USA
| | - Benjamin I. Laufer
- Department of Neuroscience, Genentech, South San Francisco, CA 94080, USA
- Department of OMNI Bioinformatics, Genentech, South San Francisco, CA 94080, USA
| | | | - Qingling Li
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, South San Francisco, CA 94080, USA
| | - Gaia Ruggeri
- Department of Biochemistry and Cellular Pharmacology, Genentech, South San Francisco, CA 94080, USA
| | - Maheswara Reddy Emani
- Department of Neuroscience, Genentech, South San Francisco, CA 94080, USA
- Department of Biochemistry and Cellular Pharmacology, Genentech, South San Francisco, CA 94080, USA
| | - Lilian Phu
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, South San Francisco, CA 94080, USA
| | - Brad A. Friedman
- Department of Neuroscience, Genentech, South San Francisco, CA 94080, USA
- Department of OMNI Bioinformatics, Genentech, South San Francisco, CA 94080, USA
| | - Wendy Sandoval
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, South San Francisco, CA 94080, USA
| | - Christopher M. Rose
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, South San Francisco, CA 94080, USA
| | - Hai Ngu
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Oded Foreman
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Mike Reichelt
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Yves Juste
- Department of Neuroscience, Genentech, South San Francisco, CA 94080, USA
| | - Guita Lalehzadeh
- Department of Neuroscience, Genentech, South San Francisco, CA 94080, USA
| | - Dennis Hansen
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen, 2970 Hørsholm, DK, Denmark
| | - Helle Nymark
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen, 2970 Hørsholm, DK, Denmark
| | - Denia Mellal
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen, 2970 Hørsholm, DK, Denmark
| | - Helene Gylling
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen, 2970 Hørsholm, DK, Denmark
| | - Łukasz J. Kiełpiński
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Copenhagen, 2970 Hørsholm, DK, Denmark
| | - Ben Chih
- Department of Neuroscience, Genentech, South San Francisco, CA 94080, USA
- Department of Biochemistry and Cellular Pharmacology, Genentech, South San Francisco, CA 94080, USA
| | - Baris Bingol
- Department of Neuroscience, Genentech, South San Francisco, CA 94080, USA
| | | | | | - Amy Easton
- Department of Neuroscience, Genentech, South San Francisco, CA 94080, USA
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6
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Adrian M, Weber M, Tsai MC, Glock C, Kahn OI, Phu L, Cheung TK, Meilandt WJ, Rose CM, Hoogenraad CC. Polarized microtubule remodeling transforms the morphology of reactive microglia and drives cytokine release. Nat Commun 2023; 14:6322. [PMID: 37813836 PMCID: PMC10562429 DOI: 10.1038/s41467-023-41891-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 09/19/2023] [Indexed: 10/11/2023] Open
Abstract
Microglial reactivity is a pathological hallmark in many neurodegenerative diseases. During stimulation, microglia undergo complex morphological changes, including loss of their characteristic ramified morphology, which is routinely used to detect and quantify inflammation in the brain. However, the underlying molecular mechanisms and the relation between microglial morphology and their pathophysiological function are unknown. Here, proteomic profiling of lipopolysaccharide (LPS)-reactive microglia identifies microtubule remodeling pathways as an early factor that drives the morphological change and subsequently controls cytokine responses. We find that LPS-reactive microglia reorganize their microtubules to form a stable and centrosomally-anchored array to facilitate efficient cytokine trafficking and release. We identify cyclin-dependent kinase 1 (Cdk-1) as a critical upstream regulator of microtubule remodeling and morphological change in-vitro and in-situ. Cdk-1 inhibition also rescues tau and amyloid fibril-induced morphology changes. These results demonstrate a critical role for microtubule dynamics and reorganization in microglial reactivity and modulating cytokine-mediated inflammatory responses.
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Affiliation(s)
- Max Adrian
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA, 94080, USA
- Department of Pathology, Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Martin Weber
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Ming-Chi Tsai
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Caspar Glock
- Department of OMNI Bioinformatics, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Olga I Kahn
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Lilian Phu
- Department of Microchemistry, Proteomics and Lipidomics, South San Francisco, CA, 94080, USA
| | - Tommy K Cheung
- Department of Microchemistry, Proteomics and Lipidomics, South San Francisco, CA, 94080, USA
| | - William J Meilandt
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Christopher M Rose
- Department of Microchemistry, Proteomics and Lipidomics, South San Francisco, CA, 94080, USA
| | - Casper C Hoogenraad
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA, 94080, USA.
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7
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Madsen RR, Toker A. PI3K signaling through a biochemical systems lens. J Biol Chem 2023; 299:105224. [PMID: 37673340 PMCID: PMC10570132 DOI: 10.1016/j.jbc.2023.105224] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/08/2023] Open
Abstract
Following 3 decades of extensive research into PI3K signaling, it is now evidently clear that the underlying network does not equate to a simple ON/OFF switch. This is best illustrated by the multifaceted nature of the many diseases associated with aberrant PI3K signaling, including common cancers, metabolic disease, and rare developmental disorders. However, we are still far from a complete understanding of the fundamental control principles that govern the numerous phenotypic outputs that are elicited by activation of this well-characterized biochemical signaling network, downstream of an equally diverse set of extrinsic inputs. At its core, this is a question on the role of PI3K signaling in cellular information processing and decision making. Here, we review the determinants of accurate encoding and decoding of growth factor signals and discuss outstanding questions in the PI3K signal relay network. We emphasize the importance of quantitative biochemistry, in close integration with advances in single-cell time-resolved signaling measurements and mathematical modeling.
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Affiliation(s)
- Ralitsa R Madsen
- MRC-Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom.
| | - Alex Toker
- Department of Pathology and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA.
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Sato H, Leonardi ML, Roberti SL, Jawerbaum A, Higa R. Maternal diabetes increases FOXO1 activation during embryonic cardiac development. Mol Cell Endocrinol 2023; 575:111999. [PMID: 37391062 DOI: 10.1016/j.mce.2023.111999] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/02/2023]
Abstract
Maternal diabetes is known to affect heart development, inducing the programming of cardiac alterations in the offspring's adult life. Previous studies in the heart of adult offspring have shown increased activation of FOXO1 (a transcription factor involved in a wide variety of cellular functions such as apoptosis, cellular proliferation, reactive oxygen species detoxification, and antioxidant and pro-inflammatory processes) and of target genes related to inflammatory and fibrotic processes. In this work, we aimed to evaluate the effects of maternal diabetes on FOXO1 activation as well as on the expression of target genes relevant to the formation of the cardiovascular system during organogenesis (day 12 of gestation). The embryonic heart from diabetic rats showed increased active FOXO1 levels, reduced protein levels of mTOR (a nutrient sensor regulating cell growth, proliferation and metabolism) and reduced mTORC2-SGK1 pathway, which phosphorylates FOXO1. These alterations were related to increases in the levels of 4-hydroxynonenal (an oxidative stress marker) and increased mRNA levels of inducible nitric oxide synthase, angiopoietin-2 and matrix metalloproteinase-2 (MMP2) (all FOXO1 target genes relevant for cardiac development). Results also showed increased extracellular and intracellular immunolocalization of MMP2 in the myocardium and its projection into the lumen of the cavity (trabeculations) together with decreased immunostaining of connexin 43, a protein relevant for cardiac function that is target of MMP2. In conclusion, increases in active FOXO1 induced by maternal diabetes initiate early during embryonic heart development and are related to increases in markers of oxidative stress and of proinflammatory cardiac development, as well to an altered expression of proteolytic enzymes that regulate connexin 43. These alterations may lead to an altered programming of cardiovascular development in the embryonic heart of diabetic rats.
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Affiliation(s)
- Hugo Sato
- Universidad de Buenos Aires, Facultad de Medicina, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Laboratory of Reproduction and Metabolism, CEFYBO, Buenos Aires, Argentina
| | - María Laura Leonardi
- Universidad de Buenos Aires, Facultad de Medicina, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Laboratory of Reproduction and Metabolism, CEFYBO, Buenos Aires, Argentina
| | - Sabrina Lorena Roberti
- Universidad de Buenos Aires, Facultad de Medicina, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Laboratory of Reproduction and Metabolism, CEFYBO, Buenos Aires, Argentina
| | - Alicia Jawerbaum
- Universidad de Buenos Aires, Facultad de Medicina, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Laboratory of Reproduction and Metabolism, CEFYBO, Buenos Aires, Argentina
| | - Romina Higa
- Universidad de Buenos Aires, Facultad de Medicina, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Laboratory of Reproduction and Metabolism, CEFYBO, Buenos Aires, Argentina.
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9
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Abhinand CS, Galipon J, Mori M, Ramesh P, Prasad TSK, Raju R, Sudhakaran PR, Tomita M. Temporal phosphoproteomic analysis of VEGF-A signaling in HUVECs: an insight into early signaling events associated with angiogenesis. J Cell Commun Signal 2023; 17:1067-1079. [PMID: 36881336 PMCID: PMC10409921 DOI: 10.1007/s12079-023-00736-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 02/17/2023] [Indexed: 03/08/2023] Open
Abstract
Vascular endothelial growth factor-A (VEGF-A) is one of the primary factors promoting angiogenesis in endothelial cells. Although defects in VEGF-A signaling are linked to diverse pathophysiological conditions, the early phosphorylation-dependent signaling events pertinent to VEGF-A signaling remain poorly defined. Hence, a temporal quantitative phosphoproteomic analysis was performed in human umbilical vein endothelial cells (HUVECs) treated with VEGF-A-165 for 1, 5 and 10 min. This led to the identification and quantification of 1971 unique phosphopeptides corresponding to 961 phosphoproteins and 2771 phosphorylation sites in total. Specifically, 69, 153, and 133 phosphopeptides corresponding to 62, 125, and 110 phosphoproteins respectively, were temporally phosphorylated at 1, 5, and 10 min upon addition of VEGF-A. These phosphopeptides included 14 kinases, among others. This study also captured the phosphosignaling events directed through RAC, FAK, PI3K-AKT-MTOR, ERK, and P38 MAPK modules with reference to our previously assembled VEGF-A/VEGFR2 signaling pathway map in HUVECs. Apart from a significant enrichment of biological processes such as cytoskeleton organization and actin filament binding, our results also suggest a role of AAK1-AP2M1 in the regulation of VEGFR endocytosis. Taken together, the temporal quantitative phosphoproteomics analysis of VEGF signaling in HUVECs revealed early signaling events and we believe that this analysis will serve as a starting point for the analysis of differential signaling across VEGF members toward the full elucidation of their role in the angiogenesis processes. Workflow for the identification of early phosphorylation events induced by VEGF-A-165 in HUVEC cells.
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Affiliation(s)
- Chandran S Abhinand
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan.
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India.
| | - Josephine Galipon
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan.
- Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa, 252-0882, Japan.
| | - Masaru Mori
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan
- Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa, 252-0882, Japan
| | - Poornima Ramesh
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | | | - Rajesh Raju
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
- Center for Integrative Omics Data Science, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Perumana R Sudhakaran
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, 695581, India
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan
- Department of Environment and Information Studies, Keio University, 5322 Endo, Fujisawa, Kanagawa, 252-0882, Japan
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10
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Ma TP, Izrael-Tomasevic A, Mroue R, Budayeva H, Malhotra S, Raisner R, Evangelista M, Rose CM, Kirkpatrick DS, Yu K. AzidoTMT Enables Direct Enrichment and Highly Multiplexed Quantitation of Proteome-Wide Functional Residues. J Proteome Res 2023. [PMID: 37285454 DOI: 10.1021/acs.jproteome.2c00703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Recent advances in targeted covalent inhibitors have aroused significant interest for their potential in drug development for difficult therapeutic targets. Proteome-wide profiling of functional residues is an integral step of covalent drug discovery aimed at defining actionable sites and evaluating compound selectivity in cells. A classical workflow for this purpose is called IsoTOP-ABPP, which employs an activity-based probe and two isotopically labeled azide-TEV-biotin tags to mark, enrich, and quantify proteome from two samples. Here we report a novel isobaric 11plex-AzidoTMT reagent and a new workflow, named AT-MAPP, that significantly expands multiplexing power as compared to the original isoTOP-ABPP. We demonstrate its application in identifying cysteine on- and off-targets using a KRAS G12C covalent inhibitor ARS-1620. However, changes in some of these hits can be explained by modulation at the protein and post-translational levels. Thus, it would be crucial to interrogate site-level bona fide changes in concurrence to proteome-level changes for corroboration. In addition, we perform a multiplexed covalent fragment screening using four acrylamide-based compounds as a proof-of-concept. This study identifies a diverse set of liganded cysteine residues in a compound-dependent manner with an average hit rate of 0.07% in intact cell. Lastly, we screened 20 sulfonyl fluoride-based compounds to demonstrate that the AT-MAPP assay is flexible for noncysteine functional residues such as tyrosine and lysine. Overall, we envision that 11plex-AzidoTMT will be a useful addition to the current toolbox for activity-based protein profiling and covalent drug development.
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Affiliation(s)
- Taylur P Ma
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | | | - Rana Mroue
- Department of Discovery Oncology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Hanna Budayeva
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | | | - Ryan Raisner
- Department of Discovery Oncology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Marie Evangelista
- Department of Discovery Oncology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Christopher M Rose
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Donald S Kirkpatrick
- Interline Therapeutics, Inc., South San Francisco, California 94080, United States
| | - Kebing Yu
- Fuhong Biopharma, Inc., Shanghai 201206, China
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11
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Chen JK, Merrick KA, Kong YW, Izrael-Tomasevic A, Eng G, Handly ED, Patterson JC, Cannell IG, Suarez-Lopez L, Hosios AM, Dinh A, Kirkpatrick DS, Yu K, Rose CM, Hernandez JM, Hwangbo H, Palmer AC, Vander Heiden MG, Yilmaz ÖH, Yaffe MB. An RNA Damage Response Network Mediates the Lethality of 5-FU in Clinically Relevant Tumor Types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.28.538590. [PMID: 37162991 PMCID: PMC10168374 DOI: 10.1101/2023.04.28.538590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
5-fluorouracil (5-FU) is a successful and broadly used anti-cancer therapeutic. A major mechanism of action of 5-FU is thought to be through thymidylate synthase (TYMS) inhibition resulting in dTTP depletion and activation of the DNA damage response. This suggests that 5-FU should synergize with other DNA damaging agents. However, we found that combinations of 5-FU and oxaliplatin or irinotecan failed to display any evidence of synergy in clinical trials, and resulted in sub-additive killing in a panel of colorectal cancer (CRC) cell lines. In seeking to understand this antagonism, we unexpectedly found that an RNA damage response during ribosome biogenesis dominates the drug's efficacy in tumor types for which 5-FU shows clinical benefit. 5-FU has an inherent bias for RNA incorporation, and blocking this greatly reduced drug-induced lethality, indicating that accumulation of damaged RNA is more deleterious than the lack of new RNA synthesis. Using 5-FU metabolites that specifically incorporate into either RNA or DNA revealed that CRC cell lines and patient-derived colorectal cancer organoids are inherently more sensitive to RNA damage. This difference held true in cell lines from other tissues in which 5-FU has shown clinical utility, whereas cell lines from tumor tissues that lack clinical 5-FU responsiveness typically showed greater sensitivity to the drug's DNA damage effects. Analysis of changes in the phosphoproteome and ubiquitinome shows RNA damage triggers the selective ubiquitination of multiple ribosomal proteins leading to autophagy-dependent rRNA catabolism and proteasome-dependent degradation of ubiquitinated ribosome proteins. Further, RNA damage response to 5-FU is selectively enhanced by compounds that promote ribosome biogenesis, such as KDM2A inhibitors. These results demonstrate the presence of a strong RNA damage response linked to apoptotic cell death, with clear utility of combinatorially targeting this response in cancer therapy.
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Affiliation(s)
- Jung-Kuei Chen
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Karl A. Merrick
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yi Wen Kong
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - George Eng
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Erika D. Handly
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jesse C. Patterson
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ian G. Cannell
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lucia Suarez-Lopez
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Aaron M. Hosios
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anh Dinh
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Kebing Yu
- Genentech Biotechnology company, South San Francisco, CA 94080, USA
| | | | - Jonathan M. Hernandez
- Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Haeun Hwangbo
- Curriculum in Bioinformatics and Computational Biology, UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pharmacology, Computational Medicine Program, and UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Adam C. Palmer
- Department of Pharmacology, Computational Medicine Program, and UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Matthew G. Vander Heiden
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Ömer H. Yilmaz
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael B. Yaffe
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Surgery, Beth Israel Medical Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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12
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Marei H, Tsai WTK, Kee YS, Ruiz K, He J, Cox C, Sun T, Penikalapati S, Dwivedi P, Choi M, Kan D, Saenz-Lopez P, Dorighi K, Zhang P, Kschonsak YT, Kljavin N, Amin D, Kim I, Mancini AG, Nguyen T, Wang C, Janezic E, Doan A, Mai E, Xi H, Gu C, Heinlein M, Biehs B, Wu J, Lehoux I, Harris S, Comps-Agrar L, Seshasayee D, de Sauvage FJ, Grimmer M, Li J, Agard NJ, de Sousa E Melo F. Antibody targeting of E3 ubiquitin ligases for receptor degradation. Nature 2022; 610:182-189. [PMID: 36131013 PMCID: PMC9534761 DOI: 10.1038/s41586-022-05235-6] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 08/12/2022] [Indexed: 12/31/2022]
Abstract
Most current therapies that target plasma membrane receptors function by antagonizing ligand binding or enzymatic activities. However, typical mammalian proteins comprise multiple domains that execute discrete but coordinated activities. Thus, inhibition of one domain often incompletely suppresses the function of a protein. Indeed, targeted protein degradation technologies, including proteolysis-targeting chimeras1 (PROTACs), have highlighted clinically important advantages of target degradation over inhibition2. However, the generation of heterobifunctional compounds binding to two targets with high affinity is complex, particularly when oral bioavailability is required3. Here we describe the development of proteolysis-targeting antibodies (PROTABs) that tether cell-surface E3 ubiquitin ligases to transmembrane proteins, resulting in target degradation both in vitro and in vivo. Focusing on zinc- and ring finger 3 (ZNRF3), a Wnt-responsive ligase, we show that this approach can enable colorectal cancer-specific degradation. Notably, by examining a matrix of additional cell-surface E3 ubiquitin ligases and transmembrane receptors, we demonstrate that this technology is amendable for ‘on-demand’ degradation. Furthermore, we offer insights on the ground rules governing target degradation by engineering optimized antibody formats. In summary, this work describes a strategy for the rapid development of potent, bioavailable and tissue-selective degraders of cell-surface proteins. Membrane-bound E3 ubiquitin ligases RNF43 and ZNRF3 are overexpressed in colorectal cancer, and can be repurposed using proteolysis-targeting antibodies (PROTABs) to selectively degrade cell-surface receptors in tumours.
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Affiliation(s)
- Hadir Marei
- Discovery Oncology, Genentech, South San Francisco, CA, USA
| | - Wen-Ting K Tsai
- Antibody Engineering, Genentech, South San Francisco, CA, USA
| | - Yee-Seir Kee
- Antibody Engineering, Genentech, South San Francisco, CA, USA
| | - Karen Ruiz
- Discovery Oncology, Genentech, South San Francisco, CA, USA
| | - Jieyan He
- Biochemical and Cellular Pharmacology, Genentech, South San Francisco, CA, USA
| | - Chris Cox
- Discovery Immunology, Genentech Inc, South San Francisco, CA, USA
| | - Tao Sun
- Molecular Biology, Genentech, South San Francisco, CA, USA
| | - Sai Penikalapati
- Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, USA
| | - Pankaj Dwivedi
- Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, USA
| | - Meena Choi
- Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, USA
| | - David Kan
- Translational Oncology, Genentech, South San Francisco, CA, USA
| | | | | | - Pamela Zhang
- Antibody Engineering, Genentech, South San Francisco, CA, USA
| | | | - Noelyn Kljavin
- Molecular Oncology, Genentech, South San Francisco, CA, USA
| | - Dhara Amin
- Discovery Oncology, Genentech, South San Francisco, CA, USA
| | - Ingrid Kim
- Antibody Engineering, Genentech, South San Francisco, CA, USA
| | | | - Thao Nguyen
- Molecular Oncology, Genentech, South San Francisco, CA, USA
| | - Chunling Wang
- Discovery Oncology, Genentech, South San Francisco, CA, USA
| | - Eric Janezic
- Biochemical and Cellular Pharmacology, Genentech, South San Francisco, CA, USA
| | - Alexander Doan
- Biochemical and Cellular Pharmacology, Genentech, South San Francisco, CA, USA
| | - Elaine Mai
- Biochemical and Cellular Pharmacology, Genentech, South San Francisco, CA, USA
| | - Hongkang Xi
- Antibody discovery, Genentech, South San Francisco, CA, USA
| | - Chen Gu
- Protein Chemistry, Genentech, South San Francisco, CA, USA
| | | | - Brian Biehs
- Molecular Oncology, Genentech, South San Francisco, CA, USA
| | - Jia Wu
- Antibody discovery, Genentech, South San Francisco, CA, USA
| | - Isabelle Lehoux
- Biomolecular Resources, Genentech, South San Francisco, CA, USA
| | - Seth Harris
- Structural Biology, Genentech, South San Francisco, CA, USA
| | | | | | | | | | - Jing Li
- Biochemical and Cellular Pharmacology, Genentech, South San Francisco, CA, USA
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13
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Crowl S, Jordan BT, Ahmed H, Ma CX, Naegle KM. KSTAR: An algorithm to predict patient-specific kinase activities from phosphoproteomic data. Nat Commun 2022; 13:4283. [PMID: 35879309 PMCID: PMC9314348 DOI: 10.1038/s41467-022-32017-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 07/13/2022] [Indexed: 01/09/2023] Open
Abstract
Kinase inhibitors as targeted therapies have played an important role in improving cancer outcomes. However, there are still considerable challenges, such as resistance, non-response, patient stratification, polypharmacology, and identifying combination therapy where understanding a tumor kinase activity profile could be transformative. Here, we develop a graph- and statistics-based algorithm, called KSTAR, to convert phosphoproteomic measurements of cells and tissues into a kinase activity score that is generalizable and useful for clinical pipelines, requiring no quantification of the phosphorylation sites. In this work, we demonstrate that KSTAR reliably captures expected kinase activity differences across different tissues and stimulation contexts, allows for the direct comparison of samples from independent experiments, and is robust across a wide range of dataset sizes. Finally, we apply KSTAR to clinical breast cancer phosphoproteomic data and find that there is potential for kinase activity inference from KSTAR to complement the current clinical diagnosis of HER2 status in breast cancer patients.
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Affiliation(s)
- Sam Crowl
- grid.27755.320000 0000 9136 933XUniversity of Virginia, Department of Biomedical Engineering and the Center for Public Health Genomics, Charlottesville, VA 22903 USA
| | - Ben T. Jordan
- grid.27755.320000 0000 9136 933XUniversity of Virginia, Department of Biomedical Engineering and the Center for Public Health Genomics, Charlottesville, VA 22903 USA
| | - Hamza Ahmed
- grid.27755.320000 0000 9136 933XUniversity of Virginia, Department of Biomedical Engineering and the Center for Public Health Genomics, Charlottesville, VA 22903 USA
| | - Cynthia X. Ma
- grid.4367.60000 0001 2355 7002Department of Medicine and Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63108 USA
| | - Kristen M. Naegle
- grid.27755.320000 0000 9136 933XUniversity of Virginia, Department of Biomedical Engineering and the Center for Public Health Genomics, Charlottesville, VA 22903 USA
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14
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Das A, Bhattacharya B, Roy S. Decrypting a path based approach for identifying the interplay between PI3K and GSK3 signaling cascade from the perspective of cancer. Genes Dis 2022; 9:868-888. [PMID: 35685456 PMCID: PMC9170611 DOI: 10.1016/j.gendis.2021.12.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/21/2021] [Accepted: 12/29/2021] [Indexed: 11/27/2022] Open
Abstract
Cancer is one of those leading diseases worldwide, which takes millions of lives every year. Researchers are continuously looking for specific approaches to eradicate the deadly disease, ensuring minimal adverse effects along with more therapeutic significance. Targeting of different aberrantly regulated signaling pathways, involved in cancer, is surely one of the revolutionary chemotherapeutic approach. In this instance, GSK3 and PI3K signaling cascades are considered as important role player for both the oncogenic activation and inactivation which further leads to cancer proliferation and metastasis. In this review, we have discussed the potential role of GSK3 and PI3K signaling in cancer, and we further established the crosstalk between PI3K and GSK3 signaling, through showcasing their cross activation, cross inhibition and convergence pathways in association with cancer. We also exhibited the effect of GSK3 on the efficacy of PI3K inhibitors to overcome the drug resistance and preventing the cell proliferation, metastasis in a combinatorial way with GSK3 inhibitors for a better treatment strategy in clinical settings.
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Affiliation(s)
- Abhijit Das
- Department of Pharmacology, NSHM Knowledge Campus, Kolkata- Group of Institutions, Kolkata 700053, India
| | - Barshana Bhattacharya
- Department of Pharmacology, NSHM Knowledge Campus, Kolkata- Group of Institutions, Kolkata 700053, India
| | - Souvik Roy
- Department of Pharmacology, NSHM Knowledge Campus, Kolkata- Group of Institutions, Kolkata 700053, India
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15
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The emerging role of mass spectrometry-based proteomics in drug discovery. Nat Rev Drug Discov 2022; 21:637-654. [PMID: 35351998 DOI: 10.1038/s41573-022-00409-3] [Citation(s) in RCA: 94] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2022] [Indexed: 12/14/2022]
Abstract
Proteins are the main targets of most drugs; however, system-wide methods to monitor protein activity and function are still underused in drug discovery. Novel biochemical approaches, in combination with recent developments in mass spectrometry-based proteomics instrumentation and data analysis pipelines, have now enabled the dissection of disease phenotypes and their modulation by bioactive molecules at unprecedented resolution and dimensionality. In this Review, we describe proteomics and chemoproteomics approaches for target identification and validation, as well as for identification of safety hazards. We discuss innovative strategies in early-stage drug discovery in which proteomics approaches generate unique insights, such as targeted protein degradation and the use of reactive fragments, and provide guidance for experimental strategies crucial for success.
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16
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Davies CW, Vidal SE, Phu L, Sudhamsu J, Hinkle TB, Chan Rosenberg S, Schumacher FR, Zeng YJ, Schwerdtfeger C, Peterson AS, Lill JR, Rose CM, Shaw AS, Wertz IE, Kirkpatrick DS, Koerber JT. Antibody toolkit reveals N-terminally ubiquitinated substrates of UBE2W. Nat Commun 2021; 12:4608. [PMID: 34326324 PMCID: PMC8322077 DOI: 10.1038/s41467-021-24669-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 06/28/2021] [Indexed: 02/07/2023] Open
Abstract
The ubiquitin conjugating enzyme UBE2W catalyzes non-canonical ubiquitination on the N-termini of proteins, although its substrate repertoire remains unclear. To identify endogenous N-terminally-ubiquitinated substrates, we discover four monoclonal antibodies that selectively recognize tryptic peptides with an N-terminal diglycine remnant, corresponding to sites of N-terminal ubiquitination. Importantly, these antibodies do not recognize isopeptide-linked diglycine (ubiquitin) modifications on lysine. We solve the structure of one such antibody bound to a Gly-Gly-Met peptide to reveal the molecular basis for its selective recognition. We use these antibodies in conjunction with mass spectrometry proteomics to map N-terminal ubiquitination sites on endogenous substrates of UBE2W. These substrates include UCHL1 and UCHL5, where N-terminal ubiquitination distinctly alters deubiquitinase (DUB) activity. This work describes an antibody toolkit for enrichment and global profiling of endogenous N-terminal ubiquitination sites, while revealing functionally relevant substrates of UBE2W.
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Affiliation(s)
- Christopher W. Davies
- grid.418158.10000 0004 0534 4718Department of Antibody Engineering, Genentech, Inc., South San Francisco, CA USA
| | - Simon E. Vidal
- grid.418158.10000 0004 0534 4718Departments of Molecular Oncology and Early Discovery Biochemistry, Genentech, Inc., South San Francisco, CA USA
| | - Lilian Phu
- grid.418158.10000 0004 0534 4718Department of Microchemistry, Proteomics, and Lipidomics, Genentech, Inc., South San Francisco, CA USA
| | - Jawahar Sudhamsu
- grid.418158.10000 0004 0534 4718Department of Structural Biology, Genentech, Inc., South San Francisco, CA USA
| | - Trent B. Hinkle
- grid.418158.10000 0004 0534 4718Department of Microchemistry, Proteomics, and Lipidomics, Genentech, Inc., South San Francisco, CA USA
| | - Scott Chan Rosenberg
- grid.418158.10000 0004 0534 4718Departments of Molecular Oncology and Early Discovery Biochemistry, Genentech, Inc., South San Francisco, CA USA
| | - Frances-Rose Schumacher
- grid.418158.10000 0004 0534 4718Department of Microchemistry, Proteomics, and Lipidomics, Genentech, Inc., South San Francisco, CA USA
| | - Yi Jimmy Zeng
- grid.418158.10000 0004 0534 4718Department of Microchemistry, Proteomics, and Lipidomics, Genentech, Inc., South San Francisco, CA USA
| | | | - Andrew S. Peterson
- grid.418158.10000 0004 0534 4718Department of Molecular Biology, Genentech, Inc., South San Francisco, CA USA
| | - Jennie R. Lill
- grid.418158.10000 0004 0534 4718Department of Microchemistry, Proteomics, and Lipidomics, Genentech, Inc., South San Francisco, CA USA
| | - Christopher M. Rose
- grid.418158.10000 0004 0534 4718Department of Microchemistry, Proteomics, and Lipidomics, Genentech, Inc., South San Francisco, CA USA
| | - Andrey S. Shaw
- grid.418158.10000 0004 0534 4718Research Biology, Genentech, Inc., South San Francisco, CA USA
| | - Ingrid E. Wertz
- grid.418158.10000 0004 0534 4718Departments of Molecular Oncology and Early Discovery Biochemistry, Genentech, Inc., South San Francisco, CA USA ,grid.419971.3Present Address: Bristol Myers Squibb, 1000 Sierra Point Parkway, Brisbane, CA USA
| | - Donald S. Kirkpatrick
- grid.418158.10000 0004 0534 4718Department of Microchemistry, Proteomics, and Lipidomics, Genentech, Inc., South San Francisco, CA USA ,Present Address: Interline Therapeutics, South San Francisco, CA USA
| | - James T. Koerber
- grid.418158.10000 0004 0534 4718Department of Antibody Engineering, Genentech, Inc., South San Francisco, CA USA
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17
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Rahmatbakhsh M, Gagarinova A, Babu M. Bioinformatic Analysis of Temporal and Spatial Proteome Alternations During Infections. Front Genet 2021; 12:667936. [PMID: 34276775 PMCID: PMC8283032 DOI: 10.3389/fgene.2021.667936] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 06/08/2021] [Indexed: 12/13/2022] Open
Abstract
Microbial pathogens have evolved numerous mechanisms to hijack host's systems, thus causing disease. This is mediated by alterations in the combined host-pathogen proteome in time and space. Mass spectrometry-based proteomics approaches have been developed and tailored to map disease progression. The result is complex multidimensional data that pose numerous analytic challenges for downstream interpretation. However, a systematic review of approaches for the downstream analysis of such data has been lacking in the field. In this review, we detail the steps of a typical temporal and spatial analysis, including data pre-processing steps (i.e., quality control, data normalization, the imputation of missing values, and dimensionality reduction), different statistical and machine learning approaches, validation, interpretation, and the extraction of biological information from mass spectrometry data. We also discuss current best practices for these steps based on a collection of independent studies to guide users in selecting the most suitable strategies for their dataset and analysis objectives. Moreover, we also compiled the list of commonly used R software packages for each step of the analysis. These could be easily integrated into one's analysis pipeline. Furthermore, we guide readers through various analysis steps by applying these workflows to mock and host-pathogen interaction data from public datasets. The workflows presented in this review will serve as an introduction for data analysis novices, while also helping established users update their data analysis pipelines. We conclude the review by discussing future directions and developments in temporal and spatial proteomics and data analysis approaches. Data analysis codes, prepared for this review are available from https://github.com/BabuLab-UofR/TempSpac, where guidelines and sample datasets are also offered for testing purposes.
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Affiliation(s)
| | - Alla Gagarinova
- Department of Biochemistry, Microbiology, & Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, SK, Canada
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18
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Maculins T, Verschueren E, Hinkle T, Choi M, Chang P, Chalouni C, Rao S, Kwon Y, Lim J, Katakam AK, Kunz RC, Erickson BK, Huang T, Tsai TH, Vitek O, Reichelt M, Senbabaoglu Y, Mckenzie B, Rohde JR, Dikic I, Kirkpatrick DS, Murthy A. Multiplexed proteomics of autophagy-deficient murine macrophages reveals enhanced antimicrobial immunity via the oxidative stress response. eLife 2021; 10:e62320. [PMID: 34085925 PMCID: PMC8177894 DOI: 10.7554/elife.62320] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 05/12/2021] [Indexed: 12/11/2022] Open
Abstract
Defective autophagy is strongly associated with chronic inflammation. Loss-of-function of the core autophagy gene Atg16l1 increases risk for Crohn's disease in part by enhancing innate immunity through myeloid cells such as macrophages. However, autophagy is also recognized as a mechanism for clearance of certain intracellular pathogens. These divergent observations prompted a re-evaluation of ATG16L1 in innate antimicrobial immunity. In this study, we found that loss of Atg16l1 in myeloid cells enhanced the killing of virulent Shigella flexneri (S.flexneri), a clinically relevant enteric bacterium that resides within the cytosol by escaping from membrane-bound compartments. Quantitative multiplexed proteomics of murine bone marrow-derived macrophages revealed that ATG16L1 deficiency significantly upregulated proteins involved in the glutathione-mediated antioxidant response to compensate for elevated oxidative stress, which simultaneously promoted S.flexneri killing. Consistent with this, myeloid-specific deletion of Atg16l1 in mice accelerated bacterial clearance in vitro and in vivo. Pharmacological induction of oxidative stress through suppression of cysteine import enhanced microbial clearance by macrophages. Conversely, antioxidant treatment of macrophages permitted S.flexneri proliferation. These findings demonstrate that control of oxidative stress by ATG16L1 and autophagy regulates antimicrobial immunity against intracellular pathogens.
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Affiliation(s)
- Timurs Maculins
- Department of Cancer Immunology, GenentechSouth San FranciscoUnited States
- Institute of Biochemistry II, Goethe UniversityFrankfurt am MainGermany
| | - Erik Verschueren
- Department of Microchemistry, Proteomics and Lipidomics, GenentechSouth San FranciscoUnited States
| | - Trent Hinkle
- Department of Microchemistry, Proteomics and Lipidomics, GenentechSouth San FranciscoUnited States
| | - Meena Choi
- Department of Microchemistry, Proteomics and Lipidomics, GenentechSouth San FranciscoUnited States
- Khoury College of Computer Sciences, Northeastern UniversityBostonUnited States
| | - Patrick Chang
- Department of Pathology, GenentechSouth San FranciscoUnited States
| | - Cecile Chalouni
- Department of Pathology, GenentechSouth San FranciscoUnited States
| | - Shilpa Rao
- Department of Oncology Bioinformatics, GenentechSouth San FranciscoUnited States
| | - Youngsu Kwon
- Department of Translational Immunology, GenentechSouth San FranciscoUnited States
| | - Junghyun Lim
- Department of Cancer Immunology, GenentechSouth San FranciscoUnited States
| | | | | | | | - Ting Huang
- Khoury College of Computer Sciences, Northeastern UniversityBostonUnited States
| | - Tsung-Heng Tsai
- Khoury College of Computer Sciences, Northeastern UniversityBostonUnited States
- Department of Mathematical Sciences, Kent State UniversityKentUnited States
| | - Olga Vitek
- Khoury College of Computer Sciences, Northeastern UniversityBostonUnited States
| | - Mike Reichelt
- Department of Pathology, GenentechSouth San FranciscoUnited States
| | - Yasin Senbabaoglu
- Department of Oncology Bioinformatics, GenentechSouth San FranciscoUnited States
| | - Brent Mckenzie
- Department of Translational Immunology, GenentechSouth San FranciscoUnited States
| | - John R Rohde
- Department of Microbiology and Immunology, Dalhousie UniversityHalifaxCanada
| | - Ivan Dikic
- Institute of Biochemistry II, Goethe UniversityFrankfurt am MainGermany
- Department of Infectious Diseases, GenentechSouth San FranciscoUnited States
| | | | - Aditya Murthy
- Interline TherapeuticsSouth San FranciscoUnited States
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19
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Chen H, Bühler K, Zhu Y, Nie X, Liu W. Proteomics analysis reveals the effect of 1α,25(OH) 2VD 3-glycosides on development of early testes in piglets. Sci Rep 2021; 11:11341. [PMID: 34059707 PMCID: PMC8167176 DOI: 10.1038/s41598-021-90676-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/07/2021] [Indexed: 12/31/2022] Open
Abstract
1α,25(OH)2VD3 is the most active form of VD3 in animals. It plays an important role in regulating mineral metabolism but also in reproduction. Testes are the main reproductive organs of male mammals. Our research aims to reveal the effect of 1α,25(OH)2VD3-glycosides on development of early testes in piglets. 140 weaned 21-day old piglets were selected. The piglets were randomly divided into four groups and were fed a commercial diet supplemented with 0, 1, 2 and 4 μg/kg of 1α,25(OH)2VD3, provided as 1α,25(OH)2VD3-glycosides. Sixty days after the start of the experiment, at piglet age 82 days, testes were harvested. The morphology and histology of early testicular development were assessed. In addition, the proteomic TMT/iTRAQ labelling technique was used to analyse the protein profile of the testes in each group. Western blotting was applied to verify the target of differentially abundant proteins (DAPs). The analysis of morphology and histology of testes showed that a certain concentration of 1α,25(OH)2VD3-glycosides had a positive and significant effect on testicular development. And the results of proteomics analysis showed that of the identified 132,715 peptides, 122,755 were unique peptides. 7852 proteins, of which 6573 proteins contain quantitative information. Screening for DAPs focused on proteins closely related to the regulation of testicular development such as steroid hormone synthesis, steroid biosynthesis, peroxisome and fatty acid metabolism pathways. These results indicated that 1α,25(OH)2VD3 is involved in the regulation of early testicular development in piglets. At the same time, these findings provide valuable information for the proteins involved in the regulation of testicular development, and help to better understand the mechanisms of 1α,25(OH)2VD3 in regulating the development of piglets’ testes.
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Affiliation(s)
- Haodong Chen
- College of Animal Science and Technology, Huazhong Agricultural University, Hongshan District, No.1 Shizishan Road, Wuhan, 430070, China.,National Engineering and Technology Research Center for Livestock, Wuhan, 430070, China.,The Breeding Swine Quality Supervision and Testing Center, Ministry of Agriculture, Wuhan, 430070, China
| | - Kathrin Bühler
- Herbonis Animal Health GmbH, Rheinstrasse 30, CH-4302, Augst BL, Switzerland
| | - Yan Zhu
- College of Animal Science and Technology, Huazhong Agricultural University, Hongshan District, No.1 Shizishan Road, Wuhan, 430070, China
| | - Xiongwei Nie
- College of Animal Science and Technology, Huazhong Agricultural University, Hongshan District, No.1 Shizishan Road, Wuhan, 430070, China
| | - Wanghong Liu
- College of Animal Science and Technology, Huazhong Agricultural University, Hongshan District, No.1 Shizishan Road, Wuhan, 430070, China. .,National Engineering and Technology Research Center for Livestock, Wuhan, 430070, China. .,The Breeding Swine Quality Supervision and Testing Center, Ministry of Agriculture, Wuhan, 430070, China.
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20
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mTOR Signaling in Pulmonary Vascular Disease: Pathogenic Role and Therapeutic Target. Int J Mol Sci 2021; 22:ijms22042144. [PMID: 33670032 PMCID: PMC7926633 DOI: 10.3390/ijms22042144] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 12/16/2022] Open
Abstract
Pulmonary arterial hypertension (PAH) is a progressive and fatal disease without a cure. The exact pathogenic mechanisms of PAH are complex and poorly understood, yet a number of abnormally expressed genes and regulatory pathways contribute to sustained vasoconstriction and vascular remodeling of the distal pulmonary arteries. Mammalian target of rapamycin (mTOR) is one of the major signaling pathways implicated in regulating cell proliferation, migration, differentiation, and protein synthesis. Here we will describe the canonical mTOR pathway, structural and functional differences between mTOR complexes 1 and 2, as well as the crosstalk with other important signaling cascades in the development of PAH. The pathogenic role of mTOR in pulmonary vascular remodeling and sustained vasoconstriction due to its contribution to proliferation, migration, phenotypic transition, and gene regulation in pulmonary artery smooth muscle and endothelial cells will be discussed. Despite the progress in our elucidation of the etiology and pathogenesis of PAH over the two last decades, there is a lack of effective therapeutic agents to treat PAH patients representing a significant unmet clinical need. In this review, we will explore the possibility and therapeutic potential to use inhibitors of mTOR signaling cascade to treat PAH.
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21
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Gu H, Yang K, Shen Z, Jia K, Liu P, Pan M, Sun C. ER stress-induced adipocytes secrete-aldo-keto reductase 1B7-containing exosomes that cause nonalcoholic steatohepatitis in mice. Free Radic Biol Med 2021; 163:220-233. [PMID: 33359683 DOI: 10.1016/j.freeradbiomed.2020.12.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 12/06/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022]
Abstract
Nonalcoholic steatohepatitis (NASH) is an increasingly prevalent liver disease linked to obesity and associated complications. Endoplasmic reticulum (ER) stress provokes dysfunction in lipid metabolism, which often leads to a progression of obesity-induced hepatic steatosis to NASH. However, the underlying mechanisms in which ER stress in adipose tissue induces hepatic pathology remain elusive. Here, we used male C57BL/6J mice to develop an animal model of NASH induced by a high fat (HFD) diet and methionine- and choline-deficient (MCD) diets. Using a gene-silencing approach with a recombinant lentiviral vector and extensive LC-MS/MS-based proteomics and lipidomics, we demonstrate that the ER stress-induced adipocyte-secreted exosome (ATEx) orchestrates lipid dynamics in the liver. We also noted that ATEx causes hepatic steatosis, inflammation, and fibrosis that lead to NASH through initial accumulation of glycerol and triglycerides in hepatocytes. We also determined that aldo-keto-reductase 1B7 (Akr1b7), a key mediator in liver lipid metabolism, is involved in ATEx-mediated NASH induction. Of note, Akr1b7 deficiency in ER stress-induced ATEx strongly protected the murine liver against HFD and MCD-induced NASH. Our results indicated that ER stress-induced, adipocyte-secreted ATEx triggers NASH by delivering exosomal AKR1B7 to, and elevating glycerol level, in hepatocytes. These findings suggest potential therapeutic strategie that target ATEx to prevent or manage obesity-induced NASH.
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Affiliation(s)
- Huihui Gu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Kun Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhentong Shen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Kai Jia
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ping Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Miao Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chao Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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22
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Rahman I, Athar MT, Islam M. Type 2 Diabetes, Obesity, and Cancer Share Some Common and Critical Pathways. Front Oncol 2021; 10:600824. [PMID: 33552973 PMCID: PMC7855858 DOI: 10.3389/fonc.2020.600824] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 11/24/2020] [Indexed: 12/13/2022] Open
Abstract
Diabetes and cancer are among the most frequent and complex diseases. Epidemiological evidence showed that the patients suffering from diabetes are significantly at higher risk for a number of cancer types. There are a number of evidence that support the hypothesis that these diseases are interlinked, and obesity may aggravate the risk(s) of type 2 diabetes and cancer. Multi-level unwanted alterations such as (epi-)genetic alterations, changes at the transcriptional level, and altered signaling pathways (receptor, cytoplasmic, and nuclear level) are the major source which promotes a number of complex diseases and such heterogeneous level of complexities are considered as the major barrier in the development of therapeutic agents. With so many known challenges, it is critical to understand the relationships and the commonly shared causes between type 2 diabetes and cancer, which is difficult to unravel and understand. Furthermore, the real complexity arises from contended corroborations that specific drug(s) (individually or in combination) during the treatment of type 2 diabetes may increase or decrease the cancer risk or affect cancer prognosis. In this review article, we have presented the recent and most updated evidence from the studies where the origin, biological background, the correlation between them have been presented or proved. Furthermore, we have summarized the methodological challenges and tasks that are frequently encountered. We have also outlined the physiological links between type 2 diabetes and cancers. Finally, we have presented and summarized the outline of the hallmarks for both these diseases, diabetes and cancer.
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Affiliation(s)
- Ishrat Rahman
- Department of Basic Dental Sciences, College of Dentistry, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Md Tanwir Athar
- Scientific Research Center, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Mozaffarul Islam
- Scientific Research Center, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
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23
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Anti-Angiogenic Properties of Ginsenoside Rg3. Molecules 2020; 25:molecules25214905. [PMID: 33113992 PMCID: PMC7660320 DOI: 10.3390/molecules25214905] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 12/12/2022] Open
Abstract
Ginsenoside Rg3 (Rg3) is a member of the ginsenoside family of chemicals extracted from Panax ginseng. Like other ginsenosides, Rg3 has two epimers: 20(S)-ginsenoside Rg3 (SRg3) and 20(R)-ginsenoside Rg3 (RRg3). Rg3 is an intriguing molecule due to its anti-cancer properties. One facet of the anti-cancer properties of Rg3 is the anti-angiogenic action. This review describes the controversies on the effects and effective dose range of Rg3, summarizes the evidence on the efficacy of Rg3 on angiogenesis, and raises the possibility that Rg3 is a prodrug.
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24
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Budayeva HG, Kirkpatrick DS. Monitoring protein communities and their responses to therapeutics. Nat Rev Drug Discov 2020; 19:414-426. [PMID: 32139903 DOI: 10.1038/s41573-020-0063-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2020] [Indexed: 12/19/2022]
Abstract
Most therapeutics are designed to alter the activities of proteins. From metabolic enzymes to cell surface receptors, connecting the function of a protein to a cellular phenotype, to the activity of a drug and to a clinical outcome represents key mechanistic milestones during drug development. Yet, even for therapeutics with exquisite specificity, the sequence of events following target engagement can be complex. Interconnected communities of structural, metabolic and signalling proteins modulate diverse downstream effects that manifest as interindividual differences in efficacy, adverse effects and resistance to therapy. Recent advances in mass spectrometry proteomics have made it possible to decipher these complex relationships and to understand how factors such as genotype, cell type, local environment and external perturbations influence them. In this Review, we explore how proteomic technologies are expanding our understanding of protein communities and their responses to large- and small-molecule therapeutics.
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Affiliation(s)
- Hanna G Budayeva
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, USA
| | - Donald S Kirkpatrick
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, USA.
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25
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Louie S, Heidersbach A, Blanco N, Haley B, Rose CM, Liu PS, Yim M, Tang D, Lam C, Sandoval WN, Shaw D, Snedecor B, Misaghi S. Endothelial intercellular cell adhesion molecule 1 contributes to cell aggregate formation in CHO cells cultured in serum‐free media. Biotechnol Prog 2020; 36:e2951. [DOI: 10.1002/btpr.2951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/14/2019] [Accepted: 12/11/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Salina Louie
- Cell Culture DepartmentGenentech, Inc. South San Francisco California
| | - Amy Heidersbach
- Molecular Biology DepartmentGenentech, Inc. South San Francisco California
| | - Noelia Blanco
- Cell Culture DepartmentGenentech, Inc. South San Francisco California
| | - Benjamin Haley
- Molecular Biology DepartmentGenentech, Inc. South San Francisco California
| | - Christopher M. Rose
- Microchemistry Proteomic and Lipidomic (MPL) DepartmentGenentech, Inc. South San Francisco California
| | - Peter S. Liu
- Microchemistry Proteomic and Lipidomic (MPL) DepartmentGenentech, Inc. South San Francisco California
| | - Mandy Yim
- Cell Culture DepartmentGenentech, Inc. South San Francisco California
| | - Danming Tang
- Cell Culture DepartmentGenentech, Inc. South San Francisco California
| | - Cynthia Lam
- Cell Culture DepartmentGenentech, Inc. South San Francisco California
| | - Wendy N. Sandoval
- Microchemistry Proteomic and Lipidomic (MPL) DepartmentGenentech, Inc. South San Francisco California
| | - David Shaw
- Cell Culture DepartmentGenentech, Inc. South San Francisco California
| | - Brad Snedecor
- Cell Culture DepartmentGenentech, Inc. South San Francisco California
| | - Shahram Misaghi
- Cell Culture DepartmentGenentech, Inc. South San Francisco California
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26
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Evangelisti C, Chiarini F, Paganelli F, Marmiroli S, Martelli AM. Crosstalks of GSK3 signaling with the mTOR network and effects on targeted therapy of cancer. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1867:118635. [PMID: 31884070 DOI: 10.1016/j.bbamcr.2019.118635] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 12/18/2019] [Indexed: 02/06/2023]
Abstract
The introduction of therapeutics targeting specific tumor-promoting oncogenic or non-oncogenic signaling pathways has revolutionized cancer treatment. Mechanistic (previously mammalian) target of rapamycin (mTOR), a highly conserved Ser/Thr kinase, is a central hub of the phosphatidylinositol 3-kinase (PI3K)/Akt/mTOR network, one of the most frequently deregulated signaling pathways in cancer, that makes it an attractive target for therapy. Numerous mTOR inhibitors have progressed to clinical trials and two of them have been officially approved as anticancer therapeutics. However, mTOR-targeting drugs have met with a very limited success in cancer patients. Frequently, the primary impediment to a successful targeted therapy in cancer is drug-resistance, either from the very beginning of the therapy (innate resistance) or after an initial response and upon repeated drug treatment (evasive or acquired resistance). Drug-resistance leads to treatment failure and relapse/progression of the disease. Resistance to mTOR inhibitors depends, among other reasons, on activation/deactivation of several signaling pathways, included those regulated by glycogen synthase kinase-3 (GSK3), a protein that targets a vast number of substrates in its repertoire, thereby orchestrating many processes that include cell proliferation and survival, metabolism, differentiation, and stemness. A detailed knowledge of the rewiring of signaling pathways triggered by exposure to mTOR inhibitors is critical to our understanding of the consequences such perturbations cause in tumors, including the emergence of drug-resistant cells. Here, we provide the reader with an updated overview of intricate circuitries that connect mTOR and GSK3 and we relate them to the efficacy (or lack of efficacy) of mTOR inhibitors in cancer cells.
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Affiliation(s)
- Camilla Evangelisti
- CNR Institute of Molecular Genetics, 40136 Bologna, BO, Italy; IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, BO, Italy
| | - Francesca Chiarini
- CNR Institute of Molecular Genetics, 40136 Bologna, BO, Italy; IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, BO, Italy
| | - Francesca Paganelli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, 40126 Bologna, BO, Italy
| | - Sandra Marmiroli
- Department of Biomedical, Metabolical, and Neurological Sciences, University of Modena and Reggio Emilia, 41124 Modena, MO, Italy
| | - Alberto M Martelli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, 40126 Bologna, BO, Italy.
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27
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Testini C, Smith RO, Jin Y, Martinsson P, Sun Y, Hedlund M, Sáinz-Jaspeado M, Shibuya M, Hellström M, Claesson-Welsh L. Myc-dependent endothelial proliferation is controlled by phosphotyrosine 1212 in VEGF receptor-2. EMBO Rep 2019; 20:e47845. [PMID: 31545012 PMCID: PMC6832004 DOI: 10.15252/embr.201947845] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 08/18/2019] [Accepted: 08/26/2019] [Indexed: 01/05/2023] Open
Abstract
Exaggerated signaling by vascular endothelial growth factor (VEGF)‐A and its receptor, VEGFR2, in pathologies results in poor vessel function. Still, pharmacological suppression of VEGFA/VEGFR2 may aggravate disease. Delineating VEGFR2 signaling in vivo provides strategies for suppression of specific VEGFR2‐induced pathways. Three VEGFR2 tyrosine residues (Y949, Y1212, and Y1173) induce downstream signaling. Here, we show that knock‐in of phenylalanine to create VEGFR2 Y1212F in C57Bl/6 and FVB mouse strains leads to loss of growth factor receptor‐bound protein 2‐ and phosphoinositide 3′‐kinase (PI3K)p85 signaling. C57Bl/6 Vegfr2Y1212F/Y1212F show reduced embryonic endothelial cell (EC) proliferation and partial lethality. FVB Vegfr2Y1212F/Y1212F show reduced postnatal EC proliferation. Reduced EC proliferation in Vegfr2Y1212F/Y1212F explants is rescued by c‐Myc overexpression. We conclude that VEGFR2 Y1212 signaling induces activation of extracellular‐signal‐regulated kinase (ERK)1/2 and Akt pathways required for c‐Myc‐dependent gene regulation, endothelial proliferation, and vessel stability.
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Affiliation(s)
- Chiara Testini
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ross O Smith
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Yi Jin
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Pernilla Martinsson
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ying Sun
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marie Hedlund
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Miguel Sáinz-Jaspeado
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Masabumi Shibuya
- Institute of Physiology and Medicine, Jobu University, Takasaki, Gunma, Japan
| | - Mats Hellström
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lena Claesson-Welsh
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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28
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Abed M, Verschueren E, Budayeva H, Liu P, Kirkpatrick DS, Reja R, Kummerfeld SK, Webster JD, Gierke S, Reichelt M, Anderson KR, Newman RJ, Roose-Girma M, Modrusan Z, Pektas H, Maltepe E, Newton K, Dixit VM. The Gag protein PEG10 binds to RNA and regulates trophoblast stem cell lineage specification. PLoS One 2019; 14:e0214110. [PMID: 30951545 PMCID: PMC6450627 DOI: 10.1371/journal.pone.0214110] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 03/15/2019] [Indexed: 01/03/2023] Open
Abstract
Peg10 (paternally expressed gene 10) is an imprinted gene that is essential for placental development. It is thought to derive from a Ty3-gyspy LTR (long terminal repeat) retrotransposon and retains Gag and Pol-like domains. Here we show that the Gag domain of PEG10 can promote vesicle budding similar to the HIV p24 Gag protein. Expressed in a subset of mouse endocrine organs in addition to the placenta, PEG10 was identified as a substrate of the deubiquitinating enzyme USP9X. Consistent with PEG10 having a critical role in placental development, PEG10-deficient trophoblast stem cells (TSCs) exhibited impaired differentiation into placental lineages. PEG10 expressed in wild-type, differentiating TSCs was bound to many cellular RNAs including Hbegf (Heparin-binding EGF-like growth factor), which is known to play an important role in placentation. Expression of Hbegf was reduced in PEG10-deficient TSCs suggesting that PEG10 might bind to and stabilize RNAs that are critical for normal placental development.
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Affiliation(s)
- Mona Abed
- Physiological Chemistry Department, Genentech, South San Francisco, California, United States of America
| | - Erik Verschueren
- Protein Chemistry Department, Genentech, South San Francisco, California, United States of America
| | - Hanna Budayeva
- Protein Chemistry Department, Genentech, South San Francisco, California, United States of America
| | - Peter Liu
- Protein Chemistry Department, Genentech, South San Francisco, California, United States of America
| | - Donald S. Kirkpatrick
- Protein Chemistry Department, Genentech, South San Francisco, California, United States of America
| | - Rohit Reja
- Bioinformatics and Computational Biology Department, Genentech, South San Francisco, California, United States of America
| | - Sarah K. Kummerfeld
- Bioinformatics and Computational Biology Department, Genentech, South San Francisco, California, United States of America
| | - Joshua D. Webster
- Pathology Department, Genentech, South San Francisco, California, United States of America
| | - Sarah Gierke
- Pathology Department, Genentech, South San Francisco, California, United States of America
| | - Mike Reichelt
- Pathology Department, Genentech, South San Francisco, California, United States of America
| | - Keith R. Anderson
- Molecular Biology Department, Genentech, South San Francisco, California, United States of America
| | - Robert J. Newman
- Molecular Biology Department, Genentech, South San Francisco, California, United States of America
| | - Merone Roose-Girma
- Molecular Biology Department, Genentech, South San Francisco, California, United States of America
| | - Zora Modrusan
- Molecular Biology Department, Genentech, South San Francisco, California, United States of America
| | - Hazal Pektas
- The Center for Reproductive Sciences, Division of Neonatology, University of California, San Francisco, California, United States of America
| | - Emin Maltepe
- The Center for Reproductive Sciences, Division of Neonatology, University of California, San Francisco, California, United States of America
| | - Kim Newton
- Physiological Chemistry Department, Genentech, South San Francisco, California, United States of America
| | - Vishva M. Dixit
- Physiological Chemistry Department, Genentech, South San Francisco, California, United States of America
- * E-mail:
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29
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Chiarini F, Evangelisti C, Lattanzi G, McCubrey JA, Martelli AM. Advances in understanding the mechanisms of evasive and innate resistance to mTOR inhibition in cancer cells. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:1322-1337. [PMID: 30928610 DOI: 10.1016/j.bbamcr.2019.03.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/22/2019] [Accepted: 03/26/2019] [Indexed: 12/12/2022]
Abstract
The development of drug-resistance by neoplastic cells is recognized as a major cause of targeted therapy failure and disease progression. The mechanistic (previously mammalian) target of rapamycin (mTOR) is a highly conserved Ser/Thr kinase that acts as the catalytic subunit of two structurally and functionally distinct large multiprotein complexes, referred to as mTOR complex 1 (mTORC1) and mTORC2. Both mTORC1 and mTORC2 play key roles in a variety of healthy cell types/tissues by regulating physiological anabolic and catabolic processes in response to external cues. However, a body of evidence identified aberrant activation of mTOR signaling as a common event in many human tumors. Therefore, mTOR is an attractive target for therapeutic targeting in cancer and this fact has driven the development of numerous mTOR inhibitors, several of which have progressed to clinical trials. Nevertheless, mTOR inhibitors have met with a very limited success as anticancer therapeutics. Among other reasons, this failure was initially ascribed to the activation of several compensatory signaling pathways that dampen the efficacy of mTOR inhibitors. The discovery of these regulatory feedback mechanisms greatly contributed to a better understanding of cancer cell resistance to mTOR targeting agents. However, over the last few years, other mechanisms of resistance have emerged, including epigenetic alterations, compensatory metabolism rewiring and the occurrence of mTOR mutations. In this article, we provide the reader with an updated overview of the mechanisms that could explain resistance of cancer cells to the various classes of mTOR inhibitors.
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Affiliation(s)
- Francesca Chiarini
- CNR Institute of Molecular Genetics, 40136 Bologna, BO, Italy; IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, BO, Italy
| | - Camilla Evangelisti
- CNR Institute of Molecular Genetics, 40136 Bologna, BO, Italy; IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, BO, Italy
| | - Giovanna Lattanzi
- CNR Institute of Molecular Genetics, 40136 Bologna, BO, Italy; IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, BO, Italy
| | - James A McCubrey
- Department of Microbiology & Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA.
| | - Alberto M Martelli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, 40126 Bologna, BO, Italy.
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30
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Nguyen Dang A, Mun M, Rose CM, Ahyow P, Meier A, Sandoval W, Yuk IH. Interaction of cell culture process parameters for modulating mAb afucosylation. Biotechnol Bioeng 2019; 116:831-845. [DOI: 10.1002/bit.26908] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 12/08/2018] [Accepted: 12/26/2018] [Indexed: 12/13/2022]
Affiliation(s)
| | - Melissa Mun
- Cell Culture, PTD, GenentechSouth San Francisco California
| | - Christopher M. Rose
- Microchemistry, Proteomics and Lipidomics, gRED, GenentechSouth San Francisco California
| | - Patrick Ahyow
- Cell Culture, PTD, GenentechSouth San Francisco California
| | - Angela Meier
- Cell Culture, PTD, GenentechSouth San Francisco California
| | - Wendy Sandoval
- Microchemistry, Proteomics and Lipidomics, gRED, GenentechSouth San Francisco California
| | - Inn H. Yuk
- Cell Culture, PTD, GenentechSouth San Francisco California
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31
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Anania VG, Yu K, Pingitore F, Li Q, Rose CM, Liu P, Sandoval W, Herman AE, Lill JR, Mathews WR. Discovery and Qualification of Candidate Urinary Biomarkers of Disease Activity in Lupus Nephritis. J Proteome Res 2019; 18:1264-1277. [PMID: 30525646 DOI: 10.1021/acs.jproteome.8b00874] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Lupus nephritis (LN) is a severe clinical manifestation of systemic lupus erythematosus (SLE) associated with significant morbidity and mortality. Assessment of severity and activity of renal involvement in SLE requires a kidney biopsy, an invasive procedure with limited prognostic value. Noninvasive biomarkers are needed to inform treatment decisions and to monitor disease activity. Proteinuria is associated with disease progression in LN; however, the composition of the LN urinary proteome remains incompletely characterized. To address this, we profiled LN urine samples using complementary mass spectrometry-based methods: protein gel fractionation, chemical labeling using tandem mass tags, and data-independent acquisition. Combining results from these approaches yielded quantitative information on 2573 unique proteins in urine from LN patients. A multiple-reaction monitoring (MRM) method was established to confirm eight proteins in an independent cohort of LN patients, and seven proteins (transferrin, α-2-macroglobulin, haptoglobin, afamin, α-1-antitrypsin, vimentin, and ceruloplasmin) were confirmed to be elevated in LN urine compared to healthy controls. In this study, we demonstrate that deep mass spectrometry profiling of a small number of patient samples can identify high-quality biomarkers that replicate in an independent LN disease cohort. These biomarkers are being used to inform clinical biomarker strategies to support longitudinal and interventional studies focused on evaluating disease progression and treatment efficacy of novel LN therapeutics.
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Hernandez-Armenta C, Ochoa D, Gonçalves E, Saez-Rodriguez J, Beltrao P. Benchmarking substrate-based kinase activity inference using phosphoproteomic data. Bioinformatics 2018; 33:1845-1851. [PMID: 28200105 PMCID: PMC5870625 DOI: 10.1093/bioinformatics/btx082] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 02/09/2017] [Indexed: 11/13/2022] Open
Abstract
Motivation Phosphoproteomic experiments are increasingly used to study the changes in signaling occurring across different conditions. It has been proposed that changes in phosphorylation of kinase target sites can be used to infer when a kinase activity is under regulation. However, these approaches have not yet been benchmarked due to a lack of appropriate benchmarking strategies. Results We used curated phosphoproteomic experiments and a gold standard dataset containing a total of 184 kinase-condition pairs where regulation is expected to occur to benchmark and compare different kinase activity inference strategies: Z-test, Kolmogorov Smirnov test, Wilcoxon rank sum test, gene set enrichment analysis (GSEA), and a multiple linear regression model. We also tested weighted variants of the Z-test and GSEA that include information on kinase sequence specificity as proxy for affinity. Finally, we tested how the number of known substrates and the type of evidence (in vivo, in vitro or in silico) supporting these influence the predictions. Conclusions Most models performed well with the Z-test and the GSEA performing best as determined by the area under the ROC curve (Mean AUC = 0.722). Weighting kinase targets by the kinase target sequence preference improves the results marginally. However, the number of known substrates and the evidence supporting the interactions has a strong effect on the predictions. Availability and Implementation The KSEA implementation is available in https://github.com/ evocellnet/ksea. Additional data is available in http://phosfate.com Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - David Ochoa
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Emanuel Gonçalves
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Julio Saez-Rodriguez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK.,RWTH Aachen University, Faculty of Medicine, Joint Research Center for Computational Biomedicine (JRC-COMBINE), Wendlingweg 2, Aachen, Germany
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
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33
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Hassan Z, Schneeweis C, Wirth M, Veltkamp C, Dantes Z, Feuerecker B, Ceyhan GO, Knauer SK, Weichert W, Schmid RM, Stauber R, Arlt A, Krämer OH, Rad R, Reichert M, Saur D, Schneider G. MTOR inhibitor-based combination therapies for pancreatic cancer. Br J Cancer 2018; 118:366-377. [PMID: 29384525 PMCID: PMC5808033 DOI: 10.1038/bjc.2017.421] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 10/25/2017] [Accepted: 10/26/2017] [Indexed: 12/13/2022] Open
Abstract
Background: Although the mechanistic target of rapamycin (MTOR) kinase, included in the mTORC1 and mTORC2 signalling hubs, has been demonstrated to be active in a significant fraction of patients with pancreatic ductal adenocarcinoma (PDAC), the value of the kinase as a therapeutic target needs further clarification. Methods: We used Mtor floxed mice to analyse the function of the kinase in context of the pancreas at the genetic level. Using a dual-recombinase system, which is based on the flippase-FRT (Flp-FRT) and Cre-loxP recombination technologies, we generated a novel cellular model, allowing the genetic analysis of MTOR functions in tumour maintenance. Cross-species validation and pharmacological intervention studies were used to recapitulate genetic data in human models, including primary human 3D PDAC cultures. Results: Genetic deletion of the Mtor gene in the pancreas results in exocrine and endocrine insufficiency. In established murine PDAC cells, MTOR is linked to metabolic pathways and maintains the glucose uptake and growth. Importantly, blocking MTOR genetically as well as pharmacologically results in adaptive rewiring of oncogenic signalling with activation of canonical extracellular signal-regulated kinase and phosphoinositide 3-kinase-AKT pathways. We provide evidence that interfering with such adaptive signalling in murine and human PDAC models is important in a subgroup. Conclusions: Our data suggest developing dual MTORC1/TORC2 inhibitor-based therapies for subtype-specific intervention.
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Affiliation(s)
- Zonera Hassan
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, 81675 München, Germany
| | - Christian Schneeweis
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, 81675 München, Germany
| | - Matthias Wirth
- Institute of Pathology, Heinrich-Heine University and University Hospital Düsseldorf, 40225 Düsseldorf, Germany
| | - Christian Veltkamp
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, 81675 München, Germany
| | - Zahra Dantes
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, 81675 München, Germany
| | - Benedikt Feuerecker
- Department of Nuclear Medicine, Klinikum rechts der Isar, Technical University Munich, 81675 München, Germany.,German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Güralp O Ceyhan
- Department of Surgery, Klinikum rechts der Isar, Technical University of Munich, 81675 München, Germany
| | - Shirley K Knauer
- Molecular Biology, Centre for Medical Biotechnology (ZMB), University Duisburg-Essen, 45141 Essen, Germany
| | - Wilko Weichert
- Institute of Pathology, Technische Universität München, 81675 München, Germany
| | - Roland M Schmid
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, 81675 München, Germany
| | - Roland Stauber
- Molecular and Cellular Oncology/ENT, University Medical Center Mainz, Langenbeckstrasse 1, Mainz 55131, Germany
| | - Alexander Arlt
- Laboratory of Molecular Gastroenterology and Hepatology, 1st Department of Internal Medicine, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Oliver H Krämer
- Department of Toxicology, University of Mainz Medical Center, Mainz 55131, Germany
| | - Roland Rad
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, 81675 München, Germany.,German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Maximilian Reichert
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, 81675 München, Germany.,Division of Gastroenterology and Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dieter Saur
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, 81675 München, Germany.,German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Günter Schneider
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, 81675 München, Germany.,German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
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The mTOR-Bach2 Cascade Controls Cell Cycle and Class Switch Recombination during B Cell Differentiation. Mol Cell Biol 2017; 37:MCB.00418-17. [PMID: 28993481 DOI: 10.1128/mcb.00418-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 10/03/2017] [Indexed: 12/25/2022] Open
Abstract
The transcription factor Bach2 regulates both acquired and innate immunity at multiple steps, including antibody class switching and regulatory T cell development in activated B and T cells, respectively. However, little is known about the molecular mechanisms of Bach2 regulation in response to signaling of cytokines and antigen. We show here that mammalian target of rapamycin (mTOR) controls Bach2 along B cell differentiation with two distinct mechanisms in pre-B cells. First, mTOR complex 1 (mTORC1) inhibited accumulation of Bach2 protein in nuclei and reduced its stability. Second, mTOR complex 2 (mTORC2) inhibited FoxO1 to reduce Bach2 mRNA expression. Using expression profiling and chromatin immunoprecipitation assay, the Ccnd3 gene, encoding cyclin D3, was identified as a new direct target of Bach2. A proper cell cycle was lost at pre-B and mature B cell stages in Bach2-deficient mice. Furthermore, AZD8055, an mTOR inhibitor, increased class switch recombination in wild-type mature B cells but not in Bach2-deficient cells. These results suggest that the mTOR-Bach2 cascade regulates proper cell cycle arrest in B cells as well as immunoglobulin gene rearrangement.
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35
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Lue HW, Podolak J, Kolahi K, Cheng L, Rao S, Garg D, Xue CH, Rantala JK, Tyner JW, Thornburg KL, Martinez-Acevedo A, Liu JJ, Amling CL, Truillet C, Louie SM, Anderson KE, Evans MJ, O'Donnell VB, Nomura DK, Drake JM, Ritz A, Thomas GV. Metabolic reprogramming ensures cancer cell survival despite oncogenic signaling blockade. Genes Dev 2017; 31:2067-2084. [PMID: 29138276 PMCID: PMC5733498 DOI: 10.1101/gad.305292.117] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/26/2017] [Indexed: 12/19/2022]
Abstract
Lue et al. show that although inhibition of PI3K–AKT–mTOR signaling markedly decreased glycolysis and restrained tumor growth, these signaling and metabolic restrictions triggered autophagy. Survival of cancer cells was critically dependent on phospholipase A2 (PLA2) to mobilize lysophospholipids and free fatty acids to sustain fatty acid oxidation and oxidative phosphorylation. There is limited knowledge about the metabolic reprogramming induced by cancer therapies and how this contributes to therapeutic resistance. Here we show that although inhibition of PI3K–AKT–mTOR signaling markedly decreased glycolysis and restrained tumor growth, these signaling and metabolic restrictions triggered autophagy, which supplied the metabolites required for the maintenance of mitochondrial respiration and redox homeostasis. Specifically, we found that survival of cancer cells was critically dependent on phospholipase A2 (PLA2) to mobilize lysophospholipids and free fatty acids to sustain fatty acid oxidation and oxidative phosphorylation. Consistent with this, we observed significantly increased lipid droplets, with subsequent mobilization to mitochondria. These changes were abrogated in cells deficient for the essential autophagy gene ATG5. Accordingly, inhibition of PLA2 significantly decreased lipid droplets, decreased oxidative phosphorylation, and increased apoptosis. Together, these results describe how treatment-induced autophagy provides nutrients for cancer cell survival and identifies novel cotreatment strategies to override this survival advantage.
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Affiliation(s)
- Hui-Wen Lue
- Knight Comprehensive Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Jennifer Podolak
- Knight Comprehensive Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Kevin Kolahi
- Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Larry Cheng
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08903, USA
| | - Soumya Rao
- Knight Comprehensive Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Devin Garg
- Knight Comprehensive Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Chang-Hui Xue
- Knight Comprehensive Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Juha K Rantala
- Knight Comprehensive Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Jeffrey W Tyner
- Knight Comprehensive Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Kent L Thornburg
- Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Ann Martinez-Acevedo
- Department of Urology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Jen-Jane Liu
- Department of Urology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Christopher L Amling
- Department of Urology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Charles Truillet
- Department of Radiology, University of California at San Francisco School of Medicine, San Francisco, California 94107, USA
| | - Sharon M Louie
- University of California at Berkeley, Berkeley, California 94720, USA
| | | | - Michael J Evans
- Department of Radiology, University of California at San Francisco School of Medicine, San Francisco, California 94107, USA
| | - Valerie B O'Donnell
- Systems Immunity Research Institute, Cardiff University, Cardiff CF14 4XN, United Kingdom
| | - Daniel K Nomura
- University of California at Berkeley, Berkeley, California 94720, USA
| | - Justin M Drake
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08903, USA
| | - Anna Ritz
- Department of Biology, Reed College, Portland, Oregon 97202, USA
| | - George V Thomas
- Knight Comprehensive Cancer Institute, Oregon Health and Science University, Portland, Oregon 97239, USA.,Department of Pathology and Laboratory Medicine, Oregon Health and Science University, Portland, Oregon 97239, USA
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36
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Guo D, Murdoch CE, Xu H, Shi H, Duan DD, Ahmed A, Gu Y. Vascular endothelial growth factor signaling requires glycine to promote angiogenesis. Sci Rep 2017; 7:14749. [PMID: 29116138 PMCID: PMC5677092 DOI: 10.1038/s41598-017-15246-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 10/23/2017] [Indexed: 11/18/2022] Open
Abstract
Peripheral vascular occlusive disease (PVOD) is a common manifestation of atherosclerosis, and it has a high rate of morbidity. Therapeutic angiogenesis would re-establish blood perfusion and rescue ischemic tissue. Vascular endothelial growth factor (VEGF) induces angiogenesis and can potentially be used to treat ischemic diseases, yet in clinical trials VEGF has not fulfilled its full potential with side effects. Whether amino acids promote angiogenesis and the molecular mechanisms are largely unknown. Here we showed that (1) Glycine significantly promoted angiogenesis both in vitro and in vivo and effectively protected mitochondrial function. (2) Activation of glycine transporter 1(GlyT1) induced by VEGF led to an increase in intracellular glycine. (3) Glycine directly bounded to voltage dependent anion channel 1 (VDAC1) on the mitochondrial outer membrane and inhibited its opening. These original results highlight glycine as a necessary mediator in VEGF signalling via the GlyT1-glycine-mTOR-VDAC1 axis pathway. Therefore, the findings in this study are of significance providing new mechanistic insights into angiogenesis and providing better understanding of glycine function in angiogenesis, which may provide valuable information for development of novel therapeutic targets for the treatment of angiogenic vascular disorders.
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Affiliation(s)
- Dongqing Guo
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 100029, China.
| | - Colin E Murdoch
- Aston Medical Research Institute, Aston Medical School, Aston University, Birmingham, B4 7ET, UK
| | - Hao Xu
- Molecular Pharmacology Laboratory, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Hui Shi
- Molecular Pharmacology Laboratory, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Dayue Darrel Duan
- Laboratory of Cardiovascular Phenomics, Department of Pharmacology, Centre for Cardiovascular Research, Centre for Molecular Medicine, University of Nevada School of Medicine, Reno, Nevada, 89557-0318, USA
| | - Asif Ahmed
- Aston Medical Research Institute, Aston Medical School, Aston University, Birmingham, B4 7ET, UK
| | - Yuchun Gu
- Molecular Pharmacology Laboratory, Institute of Molecular Medicine, Peking University, Beijing, 100871, China. .,Novolife Regenerative Medicine Centre, Aston Medical Research Institute, Aston Medical School, Aston University, Birmingham, B4 7ET, UK.
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37
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Frump AL, Bonnet S, de Jesus Perez VA, Lahm T. Emerging role of angiogenesis in adaptive and maladaptive right ventricular remodeling in pulmonary hypertension. Am J Physiol Lung Cell Mol Physiol 2017; 314:L443-L460. [PMID: 29097426 DOI: 10.1152/ajplung.00374.2017] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Right ventricular (RV) function is the primary prognostic factor for both morbidity and mortality in pulmonary hypertension (PH). RV hypertrophy is initially an adaptive physiological response to increased overload; however, with persistent and/or progressive afterload increase, this response frequently transitions to more pathological maladaptive remodeling. The mechanisms and disease processes underlying this transition are mostly unknown. Angiogenesis has recently emerged as a major modifier of RV adaptation in the setting of pressure overload. A novel paradigm has emerged that suggests that angiogenesis and angiogenic signaling are required for RV adaptation to afterload increases and that impaired and/or insufficient angiogenesis is a major driver of RV decompensation. Here, we summarize our current understanding of the concepts of maladaptive and adaptive RV remodeling, discuss the current literature on angiogenesis in the adapted and failing RV, and identify potential therapeutic approaches targeting angiogenesis in RV failure.
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Affiliation(s)
- Andrea L Frump
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine , Indianapolis, Indiana
| | - Sébastien Bonnet
- Pulmonary Hypertension Research Group, Institut Universitaire de Cardiologie et de Pneumologie de Québec Research Center, Laval University , Quebec City, Quebec , Canada
| | - Vinicio A de Jesus Perez
- Division of Pulmonary/Critical Care, Stanford University School of Medicine , Stanford, California.,Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine , Stanford, California
| | - Tim Lahm
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University School of Medicine , Indianapolis, Indiana.,Richard L. Roudebush Veterans Affairs Medical Center , Indianapolis, Indiana.,Department of Cellular and Integrative Physiology, Indiana University School of Medicine , Indianapolis, Indiana
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38
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Evolving Significance and Future Relevance of Anti-Angiogenic Activity of mTOR Inhibitors in Cancer Therapy. Cancers (Basel) 2017; 9:cancers9110152. [PMID: 29104248 PMCID: PMC5704170 DOI: 10.3390/cancers9110152] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 10/23/2017] [Accepted: 10/27/2017] [Indexed: 12/12/2022] Open
Abstract
mTOR inhibitors have demonstrated remarkable anti-tumor activity in experimental models, mainly by reducing cancer cell growth and tumor angiogenesis. Their use in cancer patients as monotherapy has, however, generated only limited benefits, increasing median overall survival by only a few months. Likewise, in other targeted therapies, cancer cells develop resistance mechanisms to overcome mTOR inhibition. Hence, novel therapeutic strategies have to be designed to increase the efficacy of mTOR inhibitors in cancer. In this review, we discuss the present and future relevance of mTOR inhibitors in cancer therapy by focusing on their effects on tumor angiogenesis.
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39
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AKT/PKB Signaling: Navigating the Network. Cell 2017; 169:381-405. [PMID: 28431241 DOI: 10.1016/j.cell.2017.04.001] [Citation(s) in RCA: 2252] [Impact Index Per Article: 321.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 03/29/2017] [Accepted: 03/31/2017] [Indexed: 12/14/2022]
Abstract
The Ser and Thr kinase AKT, also known as protein kinase B (PKB), was discovered 25 years ago and has been the focus of tens of thousands of studies in diverse fields of biology and medicine. There have been many advances in our knowledge of the upstream regulatory inputs into AKT, key multifunctional downstream signaling nodes (GSK3, FoxO, mTORC1), which greatly expand the functional repertoire of AKT, and the complex circuitry of this dynamically branching and looping signaling network that is ubiquitous to nearly every cell in our body. Mouse and human genetic studies have also revealed physiological roles for the AKT network in nearly every organ system. Our comprehension of AKT regulation and functions is particularly important given the consequences of AKT dysfunction in diverse pathological settings, including developmental and overgrowth syndromes, cancer, cardiovascular disease, insulin resistance and type 2 diabetes, inflammatory and autoimmune disorders, and neurological disorders. There has also been much progress in developing AKT-selective small molecule inhibitors. Improved understanding of the molecular wiring of the AKT signaling network continues to make an impact that cuts across most disciplines of the biomedical sciences.
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40
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Kim LC, Cook RS, Chen J. mTORC1 and mTORC2 in cancer and the tumor microenvironment. Oncogene 2017; 36:2191-2201. [PMID: 27748764 PMCID: PMC5393956 DOI: 10.1038/onc.2016.363] [Citation(s) in RCA: 288] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/04/2016] [Accepted: 08/15/2016] [Indexed: 02/06/2023]
Abstract
The mammalian target of rapamycin (mTOR) is a crucial signaling node that integrates environmental cues to regulate cell survival, proliferation and metabolism, and is often deregulated in human cancer. mTOR kinase acts in two functionally distinct complexes, mTOR complex 1 (mTORC1) and 2 (mTORC2), whose activities and substrate specificities are regulated by complex co-factors. Deregulation of this centralized signaling pathway has been associated with a variety of human diseases including diabetes, neurodegeneration and cancer. Although mTORC1 signaling has been extensively studied in cancer, recent discoveries indicate a subset of human cancers harboring amplifications in mTORC2-specific genes as the only actionable genomic alterations, suggesting a distinct role for mTORC2 in cancer as well. This review will summarize recent advances in dissecting the relative contributions of mTORC1 versus mTORC2 in cancer, their role in tumor-associated blood vessels and tumor immunity, and provide an update on mTOR inhibitors.
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Affiliation(s)
- Laura C. Kim
- Department of Cancer Biology, Vanderbilt University, Nashville, TN 37232
| | - Rebecca S. Cook
- Department of Cancer Biology, Vanderbilt University, Nashville, TN 37232
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN 37232
| | - Jin Chen
- Department of Cancer Biology, Vanderbilt University, Nashville, TN 37232
- Division of Rheumatology and Immunology, Department of Medicine, Vanderbilt University, Nashville, TN 37232
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN 37232
- Department of Cell & Developmental Biology, Vanderbilt University, Nashville, TN 37232
- Veterans Affairs Medical Center, Tennessee Valley Healthcare System, Nashville, TN 37212
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41
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Abstract
Vascular endothelial growth factors (VEGFs) and their receptors (VEGFRs) are uniquely required to balance the formation of new blood vessels with the maintenance and remodelling of existing ones, during development and in adult tissues. Recent advances have greatly expanded our understanding of the tight and multi-level regulation of VEGFR2 signalling, which is the primary focus of this Review. Important insights have been gained into the regulatory roles of VEGFR-interacting proteins (such as neuropilins, proteoglycans, integrins and protein tyrosine phosphatases); the dynamics of VEGFR2 endocytosis, trafficking and signalling; and the crosstalk between VEGF-induced signalling and other endothelial signalling cascades. A clear understanding of this multifaceted signalling web is key to successful therapeutic suppression or stimulation of vascular growth.
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42
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Anania VG, Yu K, Gnad F, Pferdehirt RR, Li H, Ma TP, Jeon D, Fortelny N, Forrest W, Ashkenazi A, Overall CM, Lill JR. Uncovering a Dual Regulatory Role for Caspases During Endoplasmic Reticulum Stress-induced Cell Death. Mol Cell Proteomics 2016; 15:2293-307. [PMID: 27125827 PMCID: PMC4937505 DOI: 10.1074/mcp.m115.055376] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Indexed: 12/13/2022] Open
Abstract
Many diseases are associated with endoplasmic reticulum (ER) stress, which results from an accumulation of misfolded proteins. This triggers an adaptive response called the "unfolded protein response" (UPR), and prolonged exposure to ER stress leads to cell death. Caspases are reported to play a critical role in ER stress-induced cell death but the underlying mechanisms by which they exert their effect continue to remain elusive. To understand the role caspases play during ER stress, a systems level approach integrating analysis of the transcriptome, proteome, and proteolytic substrate profile was employed. This quantitative analysis revealed transcriptional profiles for most human genes, provided information on protein abundance for 4476 proteins, and identified 445 caspase substrates. Based on these data sets many caspase substrates were shown to be downregulated at the protein level during ER stress suggesting caspase activity inhibits their cellular function. Additionally, RNA sequencing revealed a role for caspases in regulation of ER stress-induced transcriptional pathways and gene set enrichment analysis showed expression of multiple gene targets of essential transcription factors to be upregulated during ER stress upon inhibition of caspases. Furthermore, these transcription factors were degraded in a caspase-dependent manner during ER stress. These results indicate that caspases play a dual role in regulating the cellular response to ER stress through both post-translational and transcriptional regulatory mechanisms. Moreover, this study provides unique insight into progression of the unfolded protein response into cell death, which may help identify therapeutic strategies to treat ER stress-related diseases.
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Affiliation(s)
| | - Kebing Yu
- From the Departments of ‡Protein Chemistry
| | | | | | | | | | - Diana Jeon
- From the Departments of ‡Protein Chemistry
| | - Nikolaus Fortelny
- ‖Departments of Oral Biological and Medical Sciences, and University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Christopher M Overall
- ‖Departments of Oral Biological and Medical Sciences, and University of British Columbia, Vancouver, British Columbia, Canada
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Chidiac R, Zhang Y, Tessier S, Faubert D, Delisle C, Gratton JP. Comparative Phosphoproteomics Analysis of VEGF and Angiopoietin-1 Signaling Reveals ZO-1 as a Critical Regulator of Endothelial Cell Proliferation. Mol Cell Proteomics 2016; 15:1511-25. [PMID: 26846344 DOI: 10.1074/mcp.m115.053298] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Indexed: 12/18/2022] Open
Abstract
VEGF and angiopoietin-1 (Ang-1) are essential factors to promote angiogenesis through regulation of a plethora of signaling events in endothelial cells (ECs). Although pathways activated by VEGF and Ang-1 are being established, the unique signaling nodes conferring specific responses to each factor remain poorly defined. Thus, we conducted a large-scale comparative phosphoproteomic analysis of signaling pathways activated by VEGF and Ang-1 in ECs using mass spectrometry. Analysis of VEGF and Ang-1 networks of regulated phosphoproteins revealed that the junctional proteins ZO-1, ZO-2, JUP and p120-catenin are part of a cluster of proteins phosphorylated following VEGF stimulation that are linked to MAPK1 activation. Down-regulation of these junctional proteins led to MAPK1 activation and accordingly, increased proliferation of ECs stimulated specifically by VEGF, but not by Ang-1. We identified ZO-1 as the central regulator of this effect and showed that modulation of cellular ZO-1 levels is necessary for EC proliferation during vascular development of the mouse postnatal retina. In conclusion, we uncovered ZO-1 as part of a signaling node activated by VEGF, but not Ang-1, that specifically modulates EC proliferation during angiogenesis.
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Affiliation(s)
- Rony Chidiac
- From the ‡Department of Pharmacology, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada; §Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Ying Zhang
- From the ‡Department of Pharmacology, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada; §Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Sylvain Tessier
- ¶Proteomics discovery platform, Institut de recherches cliniques de Montréal (IRCM), Montreal, Quebec, Canada
| | - Denis Faubert
- ¶Proteomics discovery platform, Institut de recherches cliniques de Montréal (IRCM), Montreal, Quebec, Canada
| | - Chantal Delisle
- From the ‡Department of Pharmacology, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Jean-Philippe Gratton
- From the ‡Department of Pharmacology, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada;
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44
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Whole-cell biosensor for label-free detection of GPCR-mediated drug responses in personal cell lines. Biosens Bioelectron 2015; 74:233-42. [DOI: 10.1016/j.bios.2015.06.031] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 06/09/2015] [Accepted: 06/15/2015] [Indexed: 01/08/2023]
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45
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Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data. PLoS Comput Biol 2015; 11:e1004403. [PMID: 26252020 PMCID: PMC4529189 DOI: 10.1371/journal.pcbi.1004403] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 06/11/2015] [Indexed: 12/24/2022] Open
Abstract
Cell signaling underlies transcription/epigenetic control of a vast majority of cell-fate decisions. A key goal in cell signaling studies is to identify the set of kinases that underlie key signaling events. In a typical phosphoproteomics study, phosphorylation sites (substrates) of active kinases are quantified proteome-wide. By analyzing the activities of phosphorylation sites over a time-course, the temporal dynamics of signaling cascades can be elucidated. Since many substrates of a given kinase have similar temporal kinetics, clustering phosphorylation sites into distinctive clusters can facilitate identification of their respective kinases. Here we present a knowledge-based CLUster Evaluation (CLUE) approach for identifying the most informative partitioning of a given temporal phosphoproteomics data. Our approach utilizes prior knowledge, annotated kinase-substrate relationships mined from literature and curated databases, to first generate biologically meaningful partitioning of the phosphorylation sites and then determine key kinases associated with each cluster. We demonstrate the utility of the proposed approach on two time-series phosphoproteomics datasets and identify key kinases associated with human embryonic stem cell differentiation and insulin signaling pathway. The proposed approach will be a valuable resource in the identification and characterizing of signaling networks from phosphoproteomics data. A key goal in cell signaling studies is to identify the set of kinases that underlie key signaling events. Mass spectrometry-based technologies have emerged as a powerful tool to profile proteome-wide phosphorylation events in vivo at a single amino acid resolution with high precision. However, development of algorithms to analyze and identify signaling events from high-throughput phosphoproteomics data is still in its infancy. Here we propose a knowledge-based CLUster Evaluation (CLUE) approach for identifying key signaling cascades from time-series phosphoproteomics data. Our approach utilizes known kinase-substrate annotations from curated phosphoproteomics databases to first determine the optimal clustering of the phosphorylation sites and then identify enriched kinase(s). We apply CLUE on time-series phosphoproteomics datasets and identify key kinases associated with human embryonic stem cell differentiation and insulin signaling pathway.
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46
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Al-Husseini A, Kraskauskas D, Mezzaroma E, Nordio A, Farkas D, Drake JI, Abbate A, Felty Q, Voelkel NF. Vascular endothelial growth factor receptor 3 signaling contributes to angioobliterative pulmonary hypertension. Pulm Circ 2015; 5:101-16. [PMID: 25992275 DOI: 10.1086/679704] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 10/13/2014] [Indexed: 12/13/2022] Open
Abstract
The mechanisms involved in the development of severe angioobliterative pulmonary arterial hypertension (PAH) are multicellular and complex. Many of the features of human severe PAH, including angioobliteration, lung perivascular inflammation, and right heart failure, are reproduced in the Sugen 5416/chronic hypoxia (SuHx) rat model. Here we address, at first glance, the confusing and paradoxical aspect of the model, namely, that treatment of rats with the antiangiogenic vascular endothelial growth factor (VEGF) receptor 1 and 2 kinase inhibitor, Sugen 5416, when combined with chronic hypoxia, causes angioproliferative pulmonary vascular disease. We postulated that signaling through the unblocked VEGF receptor VEGFR3 (or flt4) could account for some of the pulmonary arteriolar lumen-occluding cell growth. We also considered that Sugen 5416-induced VEGFR1 and VEGFR2 blockade could alter the expression pattern of VEGF isoform proteins. Indeed, in the lungs of SuHx rats we found increased expression of the ligand proteins VEGF-C and VEGF-D as well as enhanced expression of the VEGFR3 protein. In contrast, in the failing right ventricle of SuHx rats there was a profound decrease in the expression of VEGF-B and VEGF-D in addition to the previously described reduction in VEGF-A expression. MAZ51, an inhibitor of VEGFR3 phosphorylation and VEGFR3 signaling, largely prevented the development of angioobliteration in the SuHx model; however, obliterated vessels did not reopen when animals with established PAH were treated with the VEGFR3 inhibitor. Part of the mechanism of vasoobliteration in the SuHx model occurs via VEGFR3. VEGFR1/VEGFR2 inhibition can be initially antiangiogenic by inducing lung vessel endothelial cell apoptosis; however, it can be subsequently angiogenic via VEGF-C and VEGF-D signaling through VEGFR3.
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Affiliation(s)
- Ayser Al-Husseini
- Victoria Johnson Laboratory for Lung Research, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Donatas Kraskauskas
- Victoria Johnson Laboratory for Lung Research, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Eleanora Mezzaroma
- VCU Pauley Heart Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Andrea Nordio
- VCU Pauley Heart Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Daniela Farkas
- Victoria Johnson Laboratory for Lung Research, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Jennifer I Drake
- Victoria Johnson Laboratory for Lung Research, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Antonio Abbate
- VCU Pauley Heart Center, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Quentin Felty
- Department of Environmental and Occupational Health, Florida International University, Miami, Florida, USA
| | - Norbert F Voelkel
- Victoria Johnson Laboratory for Lung Research, Virginia Commonwealth University, Richmond, Virginia, USA
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47
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Domigan CK, Warren CM, Antanesian V, Happel K, Ziyad S, Lee S, Krall A, Duan L, Torres-Collado AX, Castellani LW, Elashoff D, Christofk HR, van der Bliek AM, Potente M, Iruela-Arispe ML. Autocrine VEGF maintains endothelial survival through regulation of metabolism and autophagy. J Cell Sci 2015; 128:2236-48. [PMID: 25956888 DOI: 10.1242/jcs.163774] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 04/30/2015] [Indexed: 12/12/2022] Open
Abstract
Autocrine VEGF is necessary for endothelial survival, although the cellular mechanisms supporting this function are unknown. Here, we show that--even after full differentiation and maturation--continuous expression of VEGF by endothelial cells is needed to sustain vascular integrity and cellular viability. Depletion of VEGF from the endothelium results in mitochondria fragmentation and suppression of glucose metabolism, leading to increased autophagy that contributes to cell death. Gene-expression profiling showed that endothelial VEGF contributes to the regulation of cell cycle and mitochondrial gene clusters, as well as several--but not all--targets of the transcription factor FOXO1. Indeed, VEGF-deficient endothelium in vitro and in vivo showed increased levels of FOXO1 protein in the nucleus and cytoplasm. Silencing of FOXO1 in VEGF-depleted cells reversed expression profiles of several of the gene clusters that were de-regulated in VEGF knockdown, and rescued both cell death and autophagy phenotypes. Our data suggest that endothelial VEGF maintains vascular homeostasis through regulation of FOXO1 levels, thereby ensuring physiological metabolism and endothelial cell survival.
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Affiliation(s)
- Courtney K Domigan
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90024, USA
| | - Carmen M Warren
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90024, USA
| | - Vaspour Antanesian
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90024, USA
| | - Katharina Happel
- Angiogenesis and Metabolism Laboratory, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Safiyyah Ziyad
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90024, USA
| | - Sunyoung Lee
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90024, USA
| | - Abigail Krall
- Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Lewei Duan
- Department of Medicine Statistics Core, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Antoni X Torres-Collado
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90024, USA
| | | | - David Elashoff
- Department of Medicine Statistics Core, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Heather R Christofk
- Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Alexander M van der Bliek
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA 90024, USA Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Michael Potente
- Angiogenesis and Metabolism Laboratory, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - M Luisa Iruela-Arispe
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90024, USA Molecular Biology Institute, University of California, Los Angeles, CA 90024, USA Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA 90024, USA
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48
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Yu K, Phu L, Varfolomeev E, Bustos D, Vucic D, Kirkpatrick DS. Immunoaffinity enrichment coupled to quantitative mass spectrometry reveals ubiquitin-mediated signaling events. J Mol Biol 2015; 427:2121-34. [PMID: 25861760 DOI: 10.1016/j.jmb.2015.03.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 03/25/2015] [Accepted: 03/30/2015] [Indexed: 12/30/2022]
Abstract
Ubiquitination is one of the most prevalent posttranslational modifications in eukaryotic cells, with functional importance in protein degradation, subcellular localization and signal transduction pathways. Immunoaffinity enrichment coupled with quantitative mass spectrometry enables the in-depth characterization of protein ubiquitination events at the site-specific level. We have applied this strategy to investigate cellular response triggered by two distinct type agents: small molecule inhibitors of the tumor-associated kinases MEK and PI3K or the pro-inflammatory cytokine IL-17. Temporal profiling of protein ubiquitination events across a series of time points covering the biological response permits interrogation of signaling through thousands of quantified proteins, of which only a subset display significant and physiologically meaningful regulation. Distinctive clusters of residues within proteins can display distinct temporal patterns attributable to diverse molecular functions, although the majority of differential ubiquitination appears as a coordinated response across the modifiable residues present within an individual substrate. In cells treated with a combination of MEK and PI3K inhibitors, we found differential ubiquitination of MEK within the first hour after treatment and a series of mitochondria proteins at later time points. In the IL-17 signaling pathway, ubiquitination events on several signaling proteins including HOIL-1 and Tollip were observed. The functional relevance of these putative IL-17 mediators was subsequently validated by knockdown of HOIL-1, HOIP and TOLIP, each of which decreased IL-17-stimulated cytokine production. Together, these data validate proteomic profiling of protein ubiquitination as a viable approach for identifying dynamic signaling components in response to intracellular and extracellular perturbations.
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Affiliation(s)
- Kebing Yu
- Department of Protein Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Lilian Phu
- Department of Protein Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Eugene Varfolomeev
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Daisy Bustos
- Department of Protein Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Domagoj Vucic
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Donald S Kirkpatrick
- Department of Protein Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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49
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Regulation of endothelial cell proliferation and vascular assembly through distinct mTORC2 signaling pathways. Mol Cell Biol 2015; 35:1299-313. [PMID: 25582201 DOI: 10.1128/mcb.00306-14] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mammalian target of rapamycin (mTOR) is a serine/threonine kinase that regulates a diverse array of cellular processes, including cell growth, survival, metabolism, and cytoskeleton dynamics. mTOR functions in two distinct complexes, mTORC1 and mTORC2, whose activities and substrate specificities are regulated by complex specific cofactors, including Raptor and Rictor, respectively. Little is known regarding the relative contribution of mTORC1 versus mTORC2 in vascular endothelial cells. Using mouse models of Raptor or Rictor gene targeting, we discovered that Rictor ablation inhibited vascular endothelial growth factor (VEGF)-induced endothelial cell proliferation and assembly in vitro and angiogenesis in vivo, whereas the loss of Raptor had only a modest effect on endothelial cells (ECs). Mechanistically, the loss of Rictor reduced the phosphorylation of AKT, protein kinase Cα (PKCα), and NDRG1 without affecting the mTORC1 pathway. In contrast, the loss of Raptor increased the phosphorylation of AKT despite inhibiting the phosphorylation of S6K1, a direct target of mTORC1. Reconstitution of Rictor-null cells with myristoylated AKT (Myr-AKT) rescued vascular assembly in Rictor-deficient endothelial cells, whereas PKCα rescued proliferation defects. Furthermore, tumor neovascularization in vivo was significantly decreased upon EC-specific Rictor deletion in mice. These data indicate that mTORC2 is a critical signaling node required for VEGF-mediated angiogenesis through the regulation of AKT and PKCα in vascular endothelial cells.
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50
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Abstract
The mammalian target of rapamycin (mTOR) has emerged as a potential target for drug development, particularly due to the fact that it plays such a crucial role in cancer biology. In addition, next-generation mTOR inhibitors have become available, marking an exciting new phase in mTOR-based therapy. However, the verdict on their therapeutic efectiveness remains unclear. Here we review phosphatidylinositol-3-kinase (PI3K)/Akt/mTOR signaling as one of the primary mechanisms for sustaining tumor outgrowth and metastasis, recent advances in the development of mTOR inhibitors, and current studies addressing mTOR activation/inhibition in colorectal cancer (CRC). We will also discuss our recent comparative study of diferent mTOR inhibitors in a population of colon cancer stem cells (CSCs), and current major challenges for achieving individualized drug therapy using kinase inhibitors.
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