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Pathmanathan S, Yao Z, Coelho P, Valla R, Drecun L, Benz C, Snider J, Saraon P, Grozavu I, Kotlyar M, Jurisica I, Park M, Stagljar I. B cell linker protein (BLNK) is a regulator of Met receptor signaling and trafficking in non-small cell lung cancer. iScience 2022; 25:105419. [DOI: 10.1016/j.isci.2022.105419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/16/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
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2
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Mauvais-Jarvis F, Lange CA, Levin ER. Membrane-Initiated Estrogen, Androgen, and Progesterone Receptor Signaling in Health and Disease. Endocr Rev 2022; 43:720-742. [PMID: 34791092 PMCID: PMC9277649 DOI: 10.1210/endrev/bnab041] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Indexed: 12/15/2022]
Abstract
Rapid effects of steroid hormones were discovered in the early 1950s, but the subject was dominated in the 1970s by discoveries of estradiol and progesterone stimulating protein synthesis. This led to the paradigm that steroid hormones regulate growth, differentiation, and metabolism via binding a receptor in the nucleus. It took 30 years to appreciate not only that some cellular functions arise solely from membrane-localized steroid receptor (SR) actions, but that rapid sex steroid signaling from membrane-localized SRs is a prerequisite for the phosphorylation, nuclear import, and potentiation of the transcriptional activity of nuclear SR counterparts. Here, we provide a review and update on the current state of knowledge of membrane-initiated estrogen (ER), androgen (AR) and progesterone (PR) receptor signaling, the mechanisms of membrane-associated SR potentiation of their nuclear SR homologues, and the importance of this membrane-nuclear SR collaboration in physiology and disease. We also highlight potential clinical implications of pathway-selective modulation of membrane-associated SR.
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Affiliation(s)
- Franck Mauvais-Jarvis
- Department of Medicine, Section of Endocrinology and Metabolism, Tulane University School of Medicine, New Orleans, LA, 70112, USA.,Tulane Center of Excellence in Sex-Based Biology & Medicine, New Orleans, LA, 70112, USA.,Southeast Louisiana Veterans Affairs Medical Center, New Orleans, LA, 70119, USA
| | - Carol A Lange
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.,Department of Medicine (Division of Hematology, Oncology, and Transplantation), University of Minnesota, Minneapolis, MN 55455, USA.,Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ellis R Levin
- Division of Endocrinology, Department of Medicine, University of California, Irvine, Irvine, CA, 92697, USA.,Department of Veterans Affairs Medical Center, Long Beach, Long Beach, CA, 90822, USA
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3
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Lei M, Qu X, Dai Z, Chen R, Zhu H, Shi Z. Effects of Caponization on Growth Performance and Carcass Composition of Yangzhou Ganders. Animals (Basel) 2022; 12:ani12111364. [PMID: 35681829 PMCID: PMC9179501 DOI: 10.3390/ani12111364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/18/2022] [Accepted: 05/23/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Goose meat is recognized as one of the healthiest foods. Goose capons are specially bred and consumed in several parts of China for their high-quality meat. However, the effects of caponization on goose growth and carcass traits have remained uninvestigated, and its molecular mechanisms remain unclear. In this research, caponization lowered testosterone and increased the total cholesterol and triglyceride concentrations in serum. Caponization increased live weights by promoting food intake and abdominal fat deposition, and improved meat quality by increasing intermuscular fat. Changes in the expression of these genes indicate that caponization increases the live weight mainly by increasing fat deposition rather than muscle growth. These results expand our understanding of the mechanisms of caponization on growth performance and fat deposition in ganders. Abstract In this study, we determined the effects of caponization on the growth performance and carcass traits of Yangzhou ganders. Fifty sham operated geese (the control group) and 80 caponized geese (the caponized group) were selected at 150 days of age and reared until 240 days of age. At 210 days of age, 30 geese from the caponized group were selected and fed with testosterone propionate (testosterone group). The results showed that caponization lowered testosterone and increased the total cholesterol and triglyceride concentrations in serum, live weights, average 15 day gains, and feed intake. Abdominal fat and intramuscular fat were significantly higher in the caponized geese than in the control at 240 days. Gene expression analysis showed that caponization promoted abdominal fat deposition and intermuscular fat content by upregulating the expression of adipogenic genes in the liver, adipose tissue, and muscle tissue. The high expression of SOCS3 in the hypothalamus, liver, and muscle of caponized geese suggests that caponization may lead to negative feedback regulation and leptin resistance. Changes in the expression of these genes, along with the downregulation of PAX3 in the breast muscle and MYOG in the leg muscles, indicate that caponization increases the live weight mainly by increasing fat deposition rather than muscle growth. These results expand our understanding of the mechanisms of caponization on growth performance and fat deposition in ganders.
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Affiliation(s)
- Mingming Lei
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (M.L.); (X.Q.); (Z.D.); (R.C.)
- Key Laboratory of Crop and Livestock Integration, Ministry of Agriculture, Nanjing 210014, China
| | - Xiaolu Qu
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (M.L.); (X.Q.); (Z.D.); (R.C.)
- Key Laboratory of Crop and Livestock Integration, Ministry of Agriculture, Nanjing 210014, China
| | - Zichun Dai
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (M.L.); (X.Q.); (Z.D.); (R.C.)
- Key Laboratory of Crop and Livestock Integration, Ministry of Agriculture, Nanjing 210014, China
| | - Rong Chen
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (M.L.); (X.Q.); (Z.D.); (R.C.)
- Key Laboratory of Crop and Livestock Integration, Ministry of Agriculture, Nanjing 210014, China
| | - Huanxi Zhu
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (M.L.); (X.Q.); (Z.D.); (R.C.)
- Key Laboratory of Crop and Livestock Integration, Ministry of Agriculture, Nanjing 210014, China
- Correspondence: (H.Z.); (Z.S.); Tel.: +86-025-8439-0346 (H.Z.); +86-025-8439-0956 (Z.S.)
| | - Zhendan Shi
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (M.L.); (X.Q.); (Z.D.); (R.C.)
- Key Laboratory of Crop and Livestock Integration, Ministry of Agriculture, Nanjing 210014, China
- Correspondence: (H.Z.); (Z.S.); Tel.: +86-025-8439-0346 (H.Z.); +86-025-8439-0956 (Z.S.)
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4
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Annese T, Tamma R, Bozza M, Zito A, Ribatti D. Autocrine/Paracrine Loop Between SCF +/c-Kit + Mast Cells Promotes Cutaneous Melanoma Progression. Front Immunol 2022; 13:794974. [PMID: 35140718 PMCID: PMC8818866 DOI: 10.3389/fimmu.2022.794974] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/05/2022] [Indexed: 12/29/2022] Open
Abstract
c-Kit, or mast/stem cell growth factor receptor Kit, is a tyrosine kinase receptor structurally analogous to the colony-stimulating factor-1 (CSF-1) and platelet-derived growth factor (PDGF) CSF-1/PDGF receptor Tyr-subfamily. It binds the cytokine KITLG/SCF to regulate cell survival and proliferation, hematopoiesis, stem cell maintenance, gametogenesis, mast cell development, migration and function, and it plays an essential role in melanogenesis. SCF and c-Kit are biologically active as membrane-bound and soluble forms. They can be expressed by tumor cells and cells of the microenvironment playing a crucial role in tumor development, progression, and relapses. To date, few investigations have concerned the role of SCF+/c-Kit+ mast cells in normal, premalignant, and malignant skin lesions that resemble steps of malignant melanoma progression. In this study, by immunolabeling reactions, we demonstrated that in melanoma lesions, SCF and c-Kit were expressed in mast cells and released by themselves, suggesting an autocrine/paracrine loop might be implicated in regulatory mechanisms of neoangiogenesis and tumor progression in human melanoma.
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Affiliation(s)
- Tiziana Annese
- Department of Basic Medical Sciences, Neurosciences and Sensory Organs, University of Bari Medical School, Bari, Italy
| | - Roberto Tamma
- Department of Basic Medical Sciences, Neurosciences and Sensory Organs, University of Bari Medical School, Bari, Italy
| | - Mariella Bozza
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Alfredo Zito
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Domenico Ribatti
- Department of Basic Medical Sciences, Neurosciences and Sensory Organs, University of Bari Medical School, Bari, Italy
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5
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Mulari S, Eskin A, Lampinen M, Nummi A, Nieminen T, Teittinen K, Ojala T, Kankainen M, Vento A, Laurikka J, Kupari M, Harjula A, Tuncbag N, Kankuri E. Ischemic Heart Disease Selectively Modifies the Right Atrial Appendage Transcriptome. Front Cardiovasc Med 2021; 8:728198. [PMID: 34926599 PMCID: PMC8674465 DOI: 10.3389/fcvm.2021.728198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/01/2021] [Indexed: 11/20/2022] Open
Abstract
Background: Although many pathological changes have been associated with ischemic heart disease (IHD), molecular-level alterations specific to the ischemic myocardium and their potential to reflect disease severity or therapeutic outcome remain unclear. Currently, diagnosis occurs relatively late and evaluating disease severity is largely based on clinical symptoms, various imaging modalities, or the determination of risk factors. This study aims to identify IHD-associated signature RNAs from the atrial myocardium and evaluate their ability to reflect disease severity or cardiac surgery outcomes. Methods and Results: We collected right atrial appendage (RAA) biopsies from 40 patients with invasive coronary angiography (ICA)-positive IHD undergoing coronary artery bypass surgery and from 8 patients ICA-negative for IHD (non-IHD) undergoing valvular surgery. Following RNA sequencing, RAA transcriptomes were analyzed against 429 donors from the GTEx project without cardiac disease. The IHD transcriptome was characterized by repressed RNA expression in pathways for cell-cell contacts and mitochondrial dysfunction. Increased expressions of the CSRNP3, FUT10, SHD, NAV2-AS4, and hsa-mir-181 genes resulted in significance with the complexity of coronary artery obstructions or correlated with a functional cardiac benefit from bypass surgery. Conclusions: Our results provide an atrial myocardium-focused insight into IHD signature RNAs. The specific gene expression changes characterized here, pave the way for future disease mechanism-based identification of biomarkers for early detection and treatment of IHD.
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Affiliation(s)
- Severi Mulari
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Heart and Lung Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Arda Eskin
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University (METU), Ankara, Turkey
| | - Milla Lampinen
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Oral and Maxillofacial Diseases, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Annu Nummi
- Heart and Lung Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Tuomo Nieminen
- Heart and Lung Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kari Teittinen
- Heart and Lung Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Teija Ojala
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matti Kankainen
- Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Antti Vento
- Heart and Lung Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Jari Laurikka
- Department of Cardiothoracic Surgery, Heart Center, Tampere University Hospital, Tampere, Finland
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Markku Kupari
- Heart and Lung Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Ari Harjula
- Heart and Lung Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Nurcan Tuncbag
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University (METU), Ankara, Turkey
- Department of Chemical and Biological Engineering, College of Engineering, Koc University, Istanbul, Turkey
- School of Medicine, Koc University, Istanbul, Turkey
| | - Esko Kankuri
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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Cancer-associated mutations in the p85α N-terminal SH2 domain activate a spectrum of receptor tyrosine kinases. Proc Natl Acad Sci U S A 2021; 118:2101751118. [PMID: 34507989 PMCID: PMC8449365 DOI: 10.1073/pnas.2101751118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2021] [Indexed: 11/18/2022] Open
Abstract
Phosphoinositide 3-kinase activation typically occurs following stimulation by upstream receptor tyrosine kinases (RTKs), which alleviate p110α inhibition by p85α. p85α and p110α driver mutations have been reported to activate p110α by disrupting the inhibitory interface between p85α and p110α. This study revealed that driver mutations in the p85α N-terminal SH2 domain can enhance p110α activity by inducing the activation of multiple RTKs. Furthermore, combination treatment with RTK and AKT inhibitors provides synergistic therapeutic efficacy. This previously uncharacterized oncogenic mechanism presents the exploitable vulnerability of a class of p85α mutant tumors. The phosphoinositide 3-kinase regulatory subunit p85α is a key regulator of kinase signaling and is frequently mutated in cancers. In the present study, we showed that in addition to weakening the inhibitory interaction between p85α and p110α, a group of driver mutations in the p85α N-terminal SH2 domain activated EGFR, HER2, HER3, c-Met, and IGF-1R in a p110α-independent manner. Cancer cells expressing these mutations exhibited the activation of p110α and the AKT pathway. Interestingly, the activation of EGFR, HER2, and c-Met was attributed to the ability of driver mutations to inhibit HER3 ubiquitination and degradation. The resulting increase in HER3 protein levels promoted its heterodimerization with EGFR, HER2, and c-Met, as well as the allosteric activation of these dimerized partners; however, HER3 silencing abolished this transactivation. Accordingly, inhibitors of either AKT or the HER family reduced the oncogenicity of driver mutations. The combination of these inhibitors resulted in marked synergy. Taken together, our findings provide mechanistic insights and suggest therapeutic strategies targeting a class of recurrent p85α mutations.
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7
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Ahmed J, Meszaros A, Lazar T, Tompa P. DNA-binding domain as the minimal region driving RNA-dependent liquid-liquid phase separation of androgen receptor. Protein Sci 2021; 30:1380-1392. [PMID: 33938068 PMCID: PMC8197421 DOI: 10.1002/pro.4100] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 12/19/2022]
Abstract
Androgen receptor (AR) is a nuclear hormone receptor that regulates the transcription of genes involved in the development of testis, prostate and the nervous system. Misregulation of AR is a major driver of prostate cancer (PC). The primary agonist of full-length AR is testosterone, whereas its splice variants, for example, AR-v7 implicated in cancer may lack a ligand-binding domain and are thus devoid of proper hormonal control. Recently, it was demonstrated that full-length AR, but not AR-v7, can undergo liquid-liquid phase separation (LLPS) in a cellular model of PC. In a detailed bioinformatics and deletion analysis, we have analyzed which AR region is responsible for LLPS. We found that its DNA-binding domain (DBD) can bind RNA and can undergo RNA-dependent LLPS. RNA regulates its LLPS in a reentrant manner, that is, it has an inhibitory effect at higher concentrations. As RNA binds DBD more weakly than DNA, while both RNA and DNA localizes into AR droplets, its LLPS depends on the relative concentration of the two nucleic acids. The region immediately preceding DBD has no effect on the LLPS propensity of AR, whereas the functional part of its long N-terminal disordered transactivation domain termed activation function 1 (AF1) inhibits AR-v7 phase separation. We suggest that the resulting diminished LLPS tendency of AR-v7 may contribute to the misregulation of the transcription function of AR in prostate cancer.
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Affiliation(s)
- Junaid Ahmed
- VIB‐VUB Center for Structural Biology, Vlaams Instituut voor BiotechnologyBrusselsBelgium
- Structural Biology Brussels (SBB), Bioengineering Sciences DepartmentVrije Universiteit Brussel (VUB)BrusselsBelgium
| | - Attila Meszaros
- VIB‐VUB Center for Structural Biology, Vlaams Instituut voor BiotechnologyBrusselsBelgium
- Structural Biology Brussels (SBB), Bioengineering Sciences DepartmentVrije Universiteit Brussel (VUB)BrusselsBelgium
| | - Tamas Lazar
- VIB‐VUB Center for Structural Biology, Vlaams Instituut voor BiotechnologyBrusselsBelgium
- Structural Biology Brussels (SBB), Bioengineering Sciences DepartmentVrije Universiteit Brussel (VUB)BrusselsBelgium
| | - Peter Tompa
- VIB‐VUB Center for Structural Biology, Vlaams Instituut voor BiotechnologyBrusselsBelgium
- Structural Biology Brussels (SBB), Bioengineering Sciences DepartmentVrije Universiteit Brussel (VUB)BrusselsBelgium
- Institute of Enzymology, Research Centre for Natural SciencesBudapestHungary
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8
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Ronan T, Garnett R, Naegle KM. New analysis pipeline for high-throughput domain-peptide affinity experiments improves SH2 interaction data. J Biol Chem 2020; 295:11346-11363. [PMID: 32540967 DOI: 10.1074/jbc.ra120.012503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 06/11/2020] [Indexed: 11/06/2022] Open
Abstract
Protein domain interactions with short linear peptides, such as those of the Src homology 2 (SH2) domain with phosphotyrosine-containing peptide motifs (pTyr), are ubiquitous and important to many biochemical processes of the cell. The desire to map and quantify these interactions has resulted in the development of high-throughput (HTP) quantitative measurement techniques, such as microarray or fluorescence polarization assays. For example, in the last 15 years, experiments have progressed from measuring single interactions to covering 500,000 of the 5.5 million possible SH2-pTyr interactions in the human proteome. However, high variability in affinity measurements and disagreements about positive interactions between published data sets led us here to reevaluate the analysis methods and raw data of published SH2-pTyr HTP experiments. We identified several opportunities for improving the identification of positive and negative interactions and the accuracy of affinity measurements. We implemented model-fitting techniques that are more statistically appropriate for the nonlinear SH2-pTyr interaction data. We also developed a method to account for protein concentration errors due to impurities and degradation or protein inactivity and aggregation. Our revised analysis increases the reported affinity accuracy, reduces the false-negative rate, and increases the amount of useful data by adding reliable true-negative results. We demonstrate improvement in classification of binding versus nonbinding when using machine-learning techniques, suggesting improved coherence in the reanalyzed data sets. We present revised SH2-pTyr affinity results and propose a new analysis pipeline for future HTP measurements of domain-peptide interactions.
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Affiliation(s)
- Tom Ronan
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Roman Garnett
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Kristen M Naegle
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
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9
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Metformin reduces HGF-induced resistance to alectinib via the inhibition of Gab1. Cell Death Dis 2020; 11:111. [PMID: 32041944 PMCID: PMC7010683 DOI: 10.1038/s41419-020-2307-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 01/17/2020] [Accepted: 01/20/2020] [Indexed: 02/02/2023]
Abstract
Alectinib is a second-generation anaplastic lymphoma kinase (ALK) inhibitor that has sufficient clinical efficacy and satisfactory safety in ALK-positive non-small cell lung cancer (NSCLC) patients with or without brain metastasis. Alectinib has now become an important drug in the first-line treatment of advanced ALK-positive NSCLC; however, resistance is almost inevitable. The increased expression of hepatocyte growth factor (HGF) and its physiological receptor tyrosine kinase MET have been shown to be linked to acquired resistance to various tyrosine kinase inhibitors (TKIs), and this phenomenon has been observed in some ALK-positive NSCLC tumour tissues. In this study, we found that HGF levels in the culture supernatant of an ALK-positive cell line tended to increase with time and could be further increased by alectinib in a time-dependent manner. Exogenous or endogenous HGF did not cause resistance to the ALK/MET double-targeted small molecule inhibitor crizotinib, but it was an important cause of alectinib resistance. Furthermore, Gab1 was a key effector in the HGF/MET signal transduction pathway that mediated alectinib resistance. The antidiabetic drug metformin combined with alectinib overcame alectinib resistance triggered by HGF/MET through disrupting the complex between MET and Gab1, thereby inhibiting Gab1 phosphorylation and the activation of downstream signal transduction pathways. These results suggest that metformin combined with alectinib may be useful for overcoming alectinib resistance induced by the activation of the HGF/MET signalling pathway and improving the efficacy of alectinib.
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10
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Proteomic Identification of Heat Shock-Induced Danger Signals in a Melanoma Cell Lysate Used in Dendritic Cell-Based Cancer Immunotherapy. J Immunol Res 2018; 2018:3982942. [PMID: 29744371 PMCID: PMC5878886 DOI: 10.1155/2018/3982942] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 11/28/2017] [Accepted: 12/11/2017] [Indexed: 12/17/2022] Open
Abstract
Autologous dendritic cells (DCs) loaded with cancer cell-derived lysates have become a promising tool in cancer immunotherapy. During the last decade, we demonstrated that vaccination of advanced melanoma patients with autologous tumor antigen presenting cells (TAPCells) loaded with an allogeneic heat shock- (HS-) conditioned melanoma cell-derived lysate (called TRIMEL) is able to induce an antitumor immune response associated with a prolonged patient survival. TRIMEL provides not only a broad spectrum of potential melanoma-associated antigens but also danger signals that are crucial in the induction of a committed mature DC phenotype. However, potential changes induced by heat conditioning on the proteome of TRIMEL are still unknown. The identification of newly or differentially expressed proteins under defined stress conditions is relevant for understanding the lysate immunogenicity. Here, we characterized the proteomic profile of TRIMEL in response to HS treatment. A quantitative label-free proteome analysis of over 2800 proteins was performed, with 91 proteins that were found to be regulated by HS treatment: 18 proteins were overexpressed and 73 underexpressed. Additionally, 32 proteins were only identified in the HS-treated TRIMEL and 26 in non HS-conditioned samples. One protein from the overexpressed group and two proteins from the HS-exclusive group were previously described as potential damage-associated molecular patterns (DAMPs). Some of the HS-induced proteins, such as haptoglobin, could be also considered as DAMPs and candidates for further immunological analysis in the establishment of new putative danger signals with immunostimulatory functions.
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11
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Huang H, Kaneko T, Sidhu SS, Li SSC. Creation of Phosphotyrosine Superbinders by Directed Evolution of an SH2 Domain. Methods Mol Biol 2017; 1555:225-254. [PMID: 28092036 DOI: 10.1007/978-1-4939-6762-9_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Commercial antibodies raised against phosphotyrosine have been widely used as reagents to detect or isolate tyrosine-phosphorylated proteins from cellular samples. However, these antibodies are costly and are not amenable to in-house production in an academic lab setting. In this chapter, we describe a method to generate super-high affinity SH2 domains, dubbed the phosphotyrosine superbinders, by evolving a natural SH2 domain using the phage display technology. The superbinders are stable and can be easily produced in Escherichia coli in large quantities. The strategy presented here may also be applied to other protein domains to generate domain variants with markedly enhanced affinities for a specific post-translational modification.
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Affiliation(s)
- Haiming Huang
- Banting and Best Department of Medical Research, University of Toronto, Donnelly Centre, 160 College Street, Toronto, ON, Canada, M5S 3E1
- Department of Molecular Genetics, University of Toronto, Donnelly Centre, 160 College Street, Toronto, ON, Canada, M5S 3E1
| | - Tomonori Kaneko
- Department of Biochemistry and Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada, N6A 5C1
| | - Sachdev S Sidhu
- Banting and Best Department of Medical Research, University of Toronto, Donnelly Centre, 160 College Street, Toronto, ON, Canada, M5S 3E1.
- Department of Molecular Genetics, University of Toronto, Donnelly Centre, 160 College Street, Toronto, ON, Canada, M5S 3E1.
| | - Shawn S C Li
- Department of Biochemistry and Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada, N6A 5C1.
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12
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Abstract
The Src Homology 2 (SH2) domain is the prototypical protein interaction module that lies at the heart of phosphotyrosine signaling. Since its serendipitous discovery, there has been a tremendous advancement in technologies and an array of techniques available for studying SH2 domains and phosphotyrosine signaling. In this chapter, we provide a glimpse of the history of SH2 domains and describe many of the tools and techniques that have been developed along the way and discuss future directions for SH2 domain studies. We highlight the gist of each chapter in this volume in the context of: the structural biology and phosphotyrosine binding; characterizing SH2 specificity and generating prediction models; systems biology and proteomics; SH2 domains in signal transduction; and SH2 domains in disease, diagnostics, and therapeutics. Many of the individual chapters provide an in-depth approach that will allow scientists to interrogate the function and role of SH2 domains.
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Affiliation(s)
- Bernard A Liu
- Broad Institute of Harvard and MIT, 415 Main St., 5175 JJ, Cambridge, MA, 02142, USA.
| | - Kazuya Machida
- Raymond and Beverly Sackler Laboratory of Genetics and Molecular Medicine, Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 400 Farmington Ave., Farmington, CT, 06030, USA.
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13
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Shah NH, Wang Q, Yan Q, Karandur D, Kadlecek TA, Fallahee IR, Russ WP, Ranganathan R, Weiss A, Kuriyan J. An electrostatic selection mechanism controls sequential kinase signaling downstream of the T cell receptor. eLife 2016; 5:e20105. [PMID: 27700984 PMCID: PMC5089863 DOI: 10.7554/elife.20105] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/03/2016] [Indexed: 12/15/2022] Open
Abstract
The sequence of events that initiates T cell signaling is dictated by the specificities and order of activation of the tyrosine kinases that signal downstream of the T cell receptor. Using a platform that combines exhaustive point-mutagenesis of peptide substrates, bacterial surface-display, cell sorting, and deep sequencing, we have defined the specificities of the first two kinases in this pathway, Lck and ZAP-70, for the T cell receptor ζ chain and the scaffold proteins LAT and SLP-76. We find that ZAP-70 selects its substrates by utilizing an electrostatic mechanism that excludes substrates with positively-charged residues and favors LAT and SLP-76 phosphosites that are surrounded by negatively-charged residues. This mechanism prevents ZAP-70 from phosphorylating its own activation loop, thereby enforcing its strict dependence on Lck for activation. The sequence features in ZAP-70, LAT, and SLP-76 that underlie electrostatic selectivity likely contribute to the specific response of T cells to foreign antigens.
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Affiliation(s)
- Neel H Shah
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
- California Institute for Quantitative Biosciences, University of California, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - Qi Wang
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
- California Institute for Quantitative Biosciences, University of California, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - Qingrong Yan
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
- California Institute for Quantitative Biosciences, University of California, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - Deepti Karandur
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
- California Institute for Quantitative Biosciences, University of California, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - Theresa A Kadlecek
- Rosalind Russell/Ephraim P Engleman Rheumatology Research Center, Department of Medicine, University of California, San Francisco, United States
- Howard Hughes Medical Institute, University of California, San Francisco, United States
| | - Ian R Fallahee
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
- California Institute for Quantitative Biosciences, University of California, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - William P Russ
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Rama Ranganathan
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, United States
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Arthur Weiss
- Rosalind Russell/Ephraim P Engleman Rheumatology Research Center, Department of Medicine, University of California, San Francisco, United States
- Howard Hughes Medical Institute, University of California, San Francisco, United States
| | - John Kuriyan
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
- California Institute for Quantitative Biosciences, University of California, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
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14
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Welsh M, Jamalpour M, Zang G, Åkerblom B. The role of the Src Homology-2 domain containing protein B (SHB) in β cells. J Mol Endocrinol 2016; 56:R21-31. [PMID: 26489764 DOI: 10.1530/jme-15-0228] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/20/2015] [Indexed: 12/17/2022]
Abstract
This review will describe the SH2-domain signaling protein Src Homology-2 domain containing protein B (SHB) and its role in various physiological processes relating in particular to glucose homeostasis and β cell function. SHB operates downstream of several tyrosine kinase receptors and assembles signaling complexes in response to receptor activation by interacting with other signaling proteins via its other domains (proline-rich, phosphotyrosine-binding and tyrosine-phosphorylation sites). The subsequent responses are context-dependent. Absence of Shb in mice has been found to exert effects on hematopoiesis, angiogenesis and glucose metabolism. Specifically, first-phase insulin secretion in response to glucose was impaired and this effect was related to altered characteristics of focal adhesion kinase activation modulating signaling through Akt, ERK, β catenin and cAMP. It is believed that SHB plays a role in integrating adaptive responses to various stimuli by simultaneously modulating cellular responses in different cell-types, thus playing a role in maintaining physiological homeostasis.
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Affiliation(s)
- Michael Welsh
- Department of Medical Cell BiologyUppsala University, PO Box 571, Husargatan 3, SE-75123 Uppsala, Sweden
| | - Maria Jamalpour
- Department of Medical Cell BiologyUppsala University, PO Box 571, Husargatan 3, SE-75123 Uppsala, Sweden
| | - Guangxiang Zang
- Department of Medical Cell BiologyUppsala University, PO Box 571, Husargatan 3, SE-75123 Uppsala, Sweden
| | - Björn Åkerblom
- Department of Medical Cell BiologyUppsala University, PO Box 571, Husargatan 3, SE-75123 Uppsala, Sweden
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15
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Ciaccio MF, Chen VC, Jones RB, Bagheri N. The DIONESUS algorithm provides scalable and accurate reconstruction of dynamic phosphoproteomic networks to reveal new drug targets. Integr Biol (Camb) 2015; 7:776-91. [PMID: 26057728 PMCID: PMC4511116 DOI: 10.1039/c5ib00065c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Many drug candidates fail in clinical trials due to an incomplete understanding of how small-molecule perturbations affect cell phenotype. Cellular responses can be non-intuitive due to systems-level properties such as redundant pathways caused by co-activation of multiple receptor tyrosine kinases. We therefore created a scalable algorithm, DIONESUS, based on partial least squares regression with variable selection to reconstruct a cellular signaling network in a human carcinoma cell line driven by EGFR overexpression. We perturbed the cells with 26 diverse growth factors and/or small molecules chosen to activate or inhibit specific subsets of receptor tyrosine kinases. We then quantified the abundance of 60 phosphosites at four time points using a modified microwestern array, a high-confidence assay of protein abundance and modification. DIONESUS, after being validated using three in silico networks, was applied to connect perturbations, phosphorylation, and cell phenotype from the high-confidence, microwestern dataset. We identified enhancement of STAT1 activity as a potential strategy to treat EGFR-hyperactive cancers and PTEN as a target of the antioxidant, N-acetylcysteine. Quantification of the relationship between drug dosage and cell viability in a panel of triple-negative breast cancer cell lines validated proposed therapeutic strategies.
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Affiliation(s)
- Mark F Ciaccio
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.
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