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Christowitz C, Olivier DW, Schneider JW, Kotze MJ, Engelbrecht AM. Incorporating functional genomics into the pathology-supported genetic testing framework implemented in South Africa: A future view of precision medicine for breast carcinomas. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2024; 793:108492. [PMID: 38631437 DOI: 10.1016/j.mrrev.2024.108492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/25/2024] [Accepted: 04/11/2024] [Indexed: 04/19/2024]
Abstract
A pathology-supported genetic testing (PSGT) framework was established in South Africa to improve access to precision medicine for patients with breast carcinomas. Nevertheless, the frequent identification of variants of uncertain significance (VUSs) with the use of genome-scale next-generation sequencing has created a bottleneck in the return of results to patients. This review highlights the importance of incorporating functional genomics into the PSGT framework as a proposed initiative. Here, we explore various model systems and experimental methods available for conducting functional studies in South Africa to enhance both variant classification and clinical interpretation. We emphasize the distinct advantages of using in vitro, in vivo, and translational ex vivo models to improve the effectiveness of precision oncology. Moreover, we highlight the relevance of methodologies such as protein modelling and structural bioinformatics, multi-omics, metabolic activity assays, flow cytometry, cell migration and invasion assays, tube-formation assays, multiplex assays of variant effect, and database mining and machine learning models. The selection of the appropriate experimental approach largely depends on the molecular mechanism of the gene under investigation and the predicted functional effect of the VUS. However, before making final decisions regarding the pathogenicity of VUSs, it is essential to assess the functional evidence and clinical outcomes under current variant interpretation guidelines. The inclusion of a functional genomics infrastructure within the PSGT framework will significantly advance the reclassification of VUSs and enhance the precision medicine pipeline for patients with breast carcinomas in South Africa.
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Affiliation(s)
- Claudia Christowitz
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch 7600, South Africa.
| | - Daniel W Olivier
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch 7600, South Africa; Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Johann W Schneider
- Division of Anatomical Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa; National Health Laboratory Service, Tygerberg Hospital, Cape Town 7505, South Africa
| | - Maritha J Kotze
- Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa; National Health Laboratory Service, Tygerberg Hospital, Cape Town 7505, South Africa
| | - Anna-Mart Engelbrecht
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch 7600, South Africa; Department of Global Health, African Cancer Institute, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
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Xie D, Wang Z, Sun B, Qu L, Zeng M, Feng L, Guo M, Wang G, Hao J, Zhou G. High frequency of alternative splicing variants of the oncogene Focal Adhesion Kinase in neuroendocrine tumors of the pancreas and breast. Front Med 2023; 17:907-923. [PMID: 37682378 DOI: 10.1007/s11684-023-1009-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/17/2023] [Indexed: 09/09/2023]
Abstract
The characteristic genetic abnormality of neuroendocrine neoplasms (NENs), a heterogeneous group of tumors found in various organs, remains to be identified. Here, based on the analysis of the splicing variants of an oncogene Focal Adhesion Kinase (FAK) in The Cancer Genome Atlas datasets that contain 9193 patients of 33 cancer subtypes, we found that Box 6/Box 7-containing FAK variants (FAK6/7) were observed in 7 (87.5%) of 8 pancreatic neuroendocrine carcinomas and 20 (11.76%) of 170 pancreatic ductal adenocarcinomas (PDACs). We tested FAK variants in 157 tumor samples collected from Chinese patients with pancreatic tumors, and found that FAK6/7 was positive in 34 (75.6%) of 45 pancreatic NENs, 19 (47.5%) of 40 pancreatic solid pseudopapillary neoplasms, and 2 (2.9%) of 69 PDACs. We further tested FAK splicing variants in breast neuroendocrine carcinoma (BrNECs), and found that FAK6/7 was positive in 14 (93.3%) of 15 BrNECs but 0 in 23 non-NEC breast cancers. We explored the underlying mechanisms and found that a splicing factor serine/arginine repetitive matrix protein 4 (SRRM4) was overexpressed in FAK6/7-positive pancreatic tumors and breast tumors, which promoted the formation of FAK6/7 in cells. These results suggested that FAK6/7 could be a biomarker of NENs and represent a potential therapeutic target for these orphan diseases.
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Affiliation(s)
- Dawei Xie
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Zheng Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Beibei Sun
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Liwei Qu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences & University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Musheng Zeng
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Lin Feng
- Department of Gastroenterology & Hepatology and Department of Pathology, Chinese People's Liberation Army General Hospital, Beijing, 100853, China
| | - Mingzhou Guo
- Department of Gastroenterology & Hepatology and Department of Pathology, Chinese People's Liberation Army General Hospital, Beijing, 100853, China.
| | - Guizhen Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Jihui Hao
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.
| | - Guangbiao Zhou
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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Bownes LV, Marayati R, Quinn CH, Hutchins SC, Stewart JE, Anderson JC, Willey CD, Datta PK, Beierle EA. Serine-Threonine Kinase Receptor Associate Protein (STRAP) confers an aggressive phenotype in neuroblastoma via regulation of Focal Adhesion Kinase (FAK). J Pediatr Surg 2022; 57:1026-1032. [PMID: 35272839 PMCID: PMC9119921 DOI: 10.1016/j.jpedsurg.2022.01.064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Serine-threonine kinase receptor associated protein (STRAP), a scaffolding protein, is upregulated in many solid tumors. As such, we hypothesized that STRAP may be overexpressed in neuroblastoma tumors and may play a role in neuroblastoma tumor progression. METHODS We examined two publicly available neuroblastoma patient databases, GSE49710 (n = 498) and GSE49711 (n = 498), to investigate STRAP expression in human specimens. SK-N-AS and SK-N-BE(2) human neuroblastoma cell lines were stably transfected with STRAP overexpression (OE) plasmid, and their resulting phenotype studied. PamChip® kinomic peptide microarray evaluated the effects of STRAP overexpression on kinase activation. RESULTS In human specimens, higher STRAP expression correlated with high-risk disease, unfavorable histology, and decreased overall neuroblastoma patient survival. STRAP OE in neuroblastoma cell lines led to increased proliferation, growth, supported a stem-like phenotype and activated downstream FAK targets. When FAK was targeted with the small molecule FAK inhibitor, PF-573,228, STRAP OE neuroblastoma cells had significantly decreased growth compared to control empty vector cells. CONCLUSION Increased STRAP expression in neuroblastoma was associated with unfavorable tumor characteristics. STRAP OE resulted in increased kinomic activity of FAK. These findings suggest that the poorer outcomes in neuroblastoma tumors associated with STRAP overexpression may be secondary to FAK activation.
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Affiliation(s)
- Laura V Bownes
- Division of Pediatric Surgery, Department of Surgery, University of Alabama at Birmingham, Birmingham, AL 35233, United States of America
| | - Raoud Marayati
- Division of Pediatric Surgery, Department of Surgery, University of Alabama at Birmingham, Birmingham, AL 35233, United States of America
| | - Colin H Quinn
- Division of Pediatric Surgery, Department of Surgery, University of Alabama at Birmingham, Birmingham, AL 35233, United States of America
| | - Sara C Hutchins
- Division of Pediatric Surgery, Department of Surgery, University of Alabama at Birmingham, Birmingham, AL 35233, United States of America
| | - Jerry E Stewart
- Division of Pediatric Surgery, Department of Surgery, University of Alabama at Birmingham, Birmingham, AL 35233, United States of America
| | - Joshua C Anderson
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, AL 35233, United States of America
| | - Christopher D Willey
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, AL 35233, United States of America
| | - Pran K Datta
- Division of Hematology and Oncology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233, United States of America
| | - Elizabeth A Beierle
- Division of Pediatric Surgery, Department of Surgery, University of Alabama at Birmingham, Birmingham, AL 35233, United States of America.
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4
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Taatjes DJ, Roth J. In focus in HCB. Histochem Cell Biol 2022; 157:123-126. [PMID: 35122121 DOI: 10.1007/s00418-022-02075-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Douglas J Taatjes
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA.
| | - Jürgen Roth
- University of Zurich, 8091, Zurich, Switzerland
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Focal adhesion kinase splicing and protein activation in papillary thyroid carcinoma progression. Histochem Cell Biol 2021; 157:183-194. [PMID: 34817652 DOI: 10.1007/s00418-021-02056-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2021] [Indexed: 01/03/2023]
Abstract
Papillary thyroid carcinoma (PTC), a common endocrine malignancy, presents a challenge from a prognostic standpoint. Molecular alterations underlying PTC progression include deregulation of focal adhesion kinase (FAK) at post-transcriptional and post-translational levels. Searching for candidate markers of PTC progression, we investigated the prognostic significance of FAK alterations on mRNA/protein level. The expression levels and subcellular localisation of auto-phosphorylated FAK (pY397-FAK) were determined by western blot (WB) and immunohistochemistry. The quantity of total FAK mRNA, alternatively spliced FAK-Del26 and FAK-Del33 variants were analysed by RT-qPCR and related to pY397-FAK expression and subcellular distribution. The results were correlated with clinicopathological parameters of the patients. The expression of pY397-FAK was significantly elevated in malignant samples. Active FAK showed predominant cytoplasmic distribution with co-occurrence along the membrane, while nuclear staining was found less frequently. Expression of pY397-FAK in separate cellular compartments correlated with adverse clinicopathological parameters, but the strongest association was found when their mean scores were calculated. Alternatively spliced FAK-Del33 and total FAK transcripts positively correlated to pY397-FAK protein levels as well as to characteristics of PTC advancement. Over-expression of FAK on mRNA (total and Del-33) and activated protein (pY397-FAK) levels is a feature of PTC advanced stages. Of the analysed alterations, the mean pY397-FAK IHC score showed the best predictive performance. Correlation between mRNA FAK-Del33 and pY397-FAK expression implies a regulatory role of alternative splicing in PTC patients.
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Rigiracciolo DC, Cirillo F, Talia M, Muglia L, Gutkind JS, Maggiolini M, Lappano R. Focal Adhesion Kinase Fine Tunes Multifaced Signals toward Breast Cancer Progression. Cancers (Basel) 2021; 13:645. [PMID: 33562737 PMCID: PMC7915897 DOI: 10.3390/cancers13040645] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 02/07/2023] Open
Abstract
Breast cancer represents the most common diagnosed malignancy and the main leading cause of tumor-related death among women worldwide. Therefore, several efforts have been made in order to identify valuable molecular biomarkers for the prognosis and prediction of therapeutic responses in breast tumor patients. In this context, emerging discoveries have indicated that focal adhesion kinase (FAK), a non-receptor tyrosine kinase, might represent a promising target involved in breast tumorigenesis. Of note, high FAK expression and activity have been tightly correlated with a poor clinical outcome and metastatic features in several tumors, including breast cancer. Recently, a role for the integrin-FAK signaling in mechanotransduction has been suggested and the function of FAK within the breast tumor microenvironment has been ascertained toward tumor angiogenesis and vascular permeability. FAK has been also involved in cancer stem cells (CSCs)-mediated initiation, maintenance and therapeutic responses of breast tumors. In addition, the potential of FAK to elicit breast tumor-promoting effects has been even associated with the capability to modulate immune responses. On the basis of these findings, several agents targeting FAK have been exploited in diverse preclinical tumor models. Here, we recapitulate the multifaceted action exerted by FAK and its prognostic significance in breast cancer. Moreover, we highlight the recent clinical evidence regarding the usefulness of FAK inhibitors in the treatment of breast tumors.
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Affiliation(s)
- Damiano Cosimo Rigiracciolo
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy; (F.C.); (M.T.); (L.M.); (R.L.)
| | - Francesca Cirillo
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy; (F.C.); (M.T.); (L.M.); (R.L.)
| | - Marianna Talia
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy; (F.C.); (M.T.); (L.M.); (R.L.)
| | - Lucia Muglia
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy; (F.C.); (M.T.); (L.M.); (R.L.)
| | - Jorge Silvio Gutkind
- Department of Pharmacology, Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA;
| | - Marcello Maggiolini
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy; (F.C.); (M.T.); (L.M.); (R.L.)
| | - Rosamaria Lappano
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy; (F.C.); (M.T.); (L.M.); (R.L.)
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Novikov NM, Zolotaryova SY, Gautreau AM, Denisov EV. Mutational drivers of cancer cell migration and invasion. Br J Cancer 2021; 124:102-114. [PMID: 33204027 PMCID: PMC7784720 DOI: 10.1038/s41416-020-01149-0] [Citation(s) in RCA: 124] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 02/06/2023] Open
Abstract
Genomic instability and mutations underlie the hallmarks of cancer-genetic alterations determine cancer cell fate by affecting cell proliferation, apoptosis and immune response, and increasing data show that mutations are involved in metastasis, a crucial event in cancer progression and a life-threatening problem in cancer patients. Invasion is the first step in the metastatic cascade, when tumour cells acquire the ability to move, penetrate into the surrounding tissue and enter lymphatic and blood vessels in order to disseminate. A role for genetic alterations in invasion is not universally accepted, with sceptics arguing that cellular motility is related only to external factors such as hypoxia, chemoattractants and the rigidity of the extracellular matrix. However, increasing evidence shows that mutations might trigger and accelerate the migration and invasion of different types of cancer cells. In this review, we summarise data from published literature on the effect of chromosomal instability and genetic mutations on cancer cell migration and invasion.
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Affiliation(s)
- Nikita M Novikov
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Sofia Y Zolotaryova
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Alexis M Gautreau
- CNRS UMR7654, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
- School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Evgeny V Denisov
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia.
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8
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RNA binding proteins: Linking mechanotransduction and tumor metastasis. Cancer Lett 2020; 496:30-40. [PMID: 33007411 DOI: 10.1016/j.canlet.2020.09.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/17/2020] [Accepted: 09/19/2020] [Indexed: 02/07/2023]
Abstract
Mechanotransduction is the leading cellular process that mammalian cells adopted to receive and respond to various mechanical cues from their local microenvironment. Increasing evidence suggests that mechano-transduction is involved in many physiological and disease conditions, ranging from early embryonic development, organogenesis, to a variety of human diseases including cancer. Mechanotransduction is mediated through several classes of senor proteins on the cell surface, intracellular signaling mediators, and core transcriptional regulation networks. Dissecting the molecular mechanisms regulating mechanotransduction and their association with cancer metastasis has received much attention in recent years. RNA binding proteins (RBPs) are a special group of nucleic acid interacting factors that participate in many important cellular processes. In this review, we would like to summarize recent research progresses in understanding the role of RBPs-mediated regulation in mechanotransduction and cancer metastasis. Those intriguing findings will provide novel insights for the disease and guide the potential development of new therapeutic approaches.
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Li BQ, Liang ZY, Seery S, Liu QF, You L, Zhang TP, Guo JC, Zhao YP. WT1 associated protein promotes metastasis and chemo-resistance to gemcitabine by stabilizing Fak mRNA in pancreatic cancer. Cancer Lett 2019; 451:48-57. [PMID: 30851419 DOI: 10.1016/j.canlet.2019.02.043] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/14/2019] [Accepted: 02/28/2019] [Indexed: 12/11/2022]
Abstract
WT1 associated protein (WTAP), playing an important role in several malignancies owing to its complex function in transcriptional and post-transcriptional regulation, is an independent prognostic indicator for pancreatic cancer (PC). However, its specific role and underlying mechanism in PC remain unclear. In the present study, we found that WTAP could promote migration/invasion and suppress chemo-sensitivity to gemcitabine in PC. Further mechanical investigation revealed that WTAP could bind to and stabilize Fak mRNA which in turn activated the Fak-PI3K-AKT and Fak-Src-GRB2-Erk1/2 signaling pathways. In addition, GSK2256098, a specific Fak inhibitor, could reverse WTAP-mediated chemo-resistance to gemcitabine and metastasis in PC. Taken together, Fak inhibitor might be a promising therapeutic option for PC patients with WTAP overexpression.
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Affiliation(s)
- Bing-Qi Li
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China.
| | - Zhi-Yong Liang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China.
| | - Samuel Seery
- School of Humanities and Social Sciences, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China.
| | - Qiao-Fei Liu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China.
| | - Lei You
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China.
| | - Tai-Ping Zhang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China.
| | - Jun-Chao Guo
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China.
| | - Yu-Pei Zhao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, China.
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Xu H, Wang Y, Lin S, Deng W, Peng D, Cui Q, Xue Y. PTMD: A Database of Human Disease-associated Post-translational Modifications. GENOMICS PROTEOMICS & BIOINFORMATICS 2018; 16:244-251. [PMID: 30244175 PMCID: PMC6205080 DOI: 10.1016/j.gpb.2018.06.004] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/04/2018] [Accepted: 06/25/2018] [Indexed: 12/20/2022]
Abstract
Various posttranslational modifications (PTMs) participate in nearly all aspects of biological processes by regulating protein functions, and aberrant states of PTMs are frequently implicated in human diseases. Therefore, an integral resource of PTM–disease associations (PDAs) would be a great help for both academic research and clinical use. In this work, we reported PTMD, a well-curated database containing PTMs that are associated with human diseases. We manually collected 1950 known PDAs in 749 proteins for 23 types of PTMs and 275 types of diseases from the literature. Database analyses show that phosphorylation has the largest number of disease associations, whereas neurologic diseases have the largest number of PTM associations. We classified all known PDAs into six classes according to the PTM status in diseases and demonstrated that the upregulation and presence of PTM events account for a predominant proportion of disease-associated PTM events. By reconstructing a disease–gene network, we observed that breast cancers have the largest number of associated PTMs and AKT1 has the largest number of PTMs connected to diseases. Finally, the PTMD database was developed with detailed annotations and can be a useful resource for further analyzing the relations between PTMs and human diseases. PTMD is freely accessible at http://ptmd.biocuckoo.org.
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Affiliation(s)
- Haodong Xu
- Department of Bioinformatics & Systems Biology, MOE Key Laboratory of Molecular Biophysics, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yongbo Wang
- Department of Bioinformatics & Systems Biology, MOE Key Laboratory of Molecular Biophysics, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Shaofeng Lin
- Department of Bioinformatics & Systems Biology, MOE Key Laboratory of Molecular Biophysics, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Wankun Deng
- Department of Bioinformatics & Systems Biology, MOE Key Laboratory of Molecular Biophysics, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Di Peng
- Department of Bioinformatics & Systems Biology, MOE Key Laboratory of Molecular Biophysics, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Qinghua Cui
- Department of Biomedical Informatics, School of Basic Medical Sciences, MOE Key Laboratory of Molecular Cardiovascular Sciences, Center for Non-coding RNA Medicine, Peking University, Beijing 100191, China.
| | - Yu Xue
- Department of Bioinformatics & Systems Biology, MOE Key Laboratory of Molecular Biophysics, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China.
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11
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Fontana R, Vivo M. Dynamics of p14ARF and Focal Adhesion Kinase-Mediated Autophagy in Cancer. Cancers (Basel) 2018; 10:cancers10070221. [PMID: 29966311 PMCID: PMC6071150 DOI: 10.3390/cancers10070221] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 06/22/2018] [Accepted: 06/26/2018] [Indexed: 12/23/2022] Open
Abstract
It has been widely shown that the focal adhesion kinase (FAK) is involved in nearly every aspect of cancer, from invasion to metastasis to epithelial–mesenchymal transition and maintenance of cancer stem cells. FAK has been shown to interact with p14ARF (alternative reading frame)—a well-established tumor suppressor—and functions in the negative regulation of cancer through both p53-dependent and -independent pathways. Interestingly, both FAK and ARF (human and mouse counterpart) proteins, as well as p53, are involved in autophagy—a process of “self-digestion”—whose main function is the recycling of cellular components and quality control of proteins and organelles. In the last years, an unexpected role of p14ARF in the survival of cancer cells has been underlined in different cellular contexts, suggesting a novel pro-oncogenic function of this protein. In this review, the mechanisms whereby ARF and FAK control autophagy are presented, as well as the role of autophagy in cell migration and spreading. Integrated investigation of these cell functions is extremely important to understand the mechanism of the basis of cell transformation and migration and thus cancer development.
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Affiliation(s)
- Rosa Fontana
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy.
| | - Maria Vivo
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy.
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12
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Yang Q, Feng M, Ma X, Li H, Xie W. Gene expression profile comparison between colorectal cancer and adjacent normal tissues. Oncol Lett 2017; 14:6071-6078. [PMID: 29113248 DOI: 10.3892/ol.2017.6915] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/13/2016] [Indexed: 01/07/2023] Open
Abstract
The present study aimed to compare gene expression profiles between colorectal cancer and adjacent normal tissues, and to perform a preliminarily analysis of the key genes and underlying molecular mechanisms implicated in colorectal cancer development. Gene expression microarray chips were used to screen genes that were differently expressed between colorectal cancer and adjacent normal tissues. Approximately 1,183 genes were differentially expressed in cancer tissues compared with adjacent normal tissues (P≤0.05; fold difference, >2.0), of which 570 genes were upregulated and 613 genes were downregulated. In total, 6 upregulated genes, including keratin 23, collagen type X α1, collagen type XI α1, cell migration-inducing hyaluronan-binding protein, transforming growth factor-β1 and V-Myc avian myelocytomatosis viral oncogene homolog, and 2 downregulated genes, including channel α subunit 7 and EPH receptor A7, were selected and validated using reverse transcription-quantitative polymerase chain reaction, which exhibited results that were consistent with the microarray analysis. These 1,183 differentially expressed genes were further classified into 71 groups based on their functions using gene ontology and pathway analyses. Kyoto Encyclopedia of Genes and Genomes analysis of these upregulated or downregulated genes suggested that 23 signaling pathways were involved. The present study preliminarily screened for and identified key genes and signaling pathways that may be closely associated with colorectal cancer development. However, subsequent gene function studies are required to verify these findings.
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Affiliation(s)
- Qian Yang
- Department of Ultrasound, Hubei Cancer Hospital, Wuhan, Hubei 430071, P.R. China
| | - Maohui Feng
- Department of Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Xiang Ma
- Department of Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Huachi Li
- Department of Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Wei Xie
- Department of Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
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Lesko AC, Prosperi JR. Epithelial Membrane Protein 2 and β1 integrin signaling regulate APC-mediated processes. Exp Cell Res 2016; 350:190-198. [PMID: 27890644 DOI: 10.1016/j.yexcr.2016.11.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/26/2016] [Accepted: 11/23/2016] [Indexed: 12/26/2022]
Abstract
Adenomatous Polyposis Coli (APC) plays a critical role in cell motility, maintenance of apical-basal polarity, and epithelial morphogenesis. We previously demonstrated that APC loss in Madin Darby Canine Kidney (MDCK) cells increases cyst size and inverts polarity independent of Wnt signaling, and upregulates the tetraspan protein, Epithelial Membrane Protein 2 (EMP2). Herein, we show that APC loss increases β1 integrin expression and migration of MDCK cells. Through 3D in vitro model systems and 2D migration analysis, we have depicted the molecular mechanism(s) by which APC influences polarity and cell motility. EMP2 knockdown in APC shRNA cells revealed that APC regulates apical-basal polarity and cyst size through EMP2. Chemical inhibition of β1 integrin and its signaling components, FAK and Src, indicated that APC controls cyst size and migration, but not polarity, through β1 integrin and its downstream targets. Combined, the current studies have identified two distinct and novel mechanisms required for APC to regulate polarity, cyst size, and cell migration independent of Wnt signaling.
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Affiliation(s)
- Alyssa C Lesko
- Department of Biological Science, Harper Cancer Research Institute, University of Notre Dame, United States
| | - Jenifer R Prosperi
- Department of Biological Science, Harper Cancer Research Institute, University of Notre Dame, United States; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, South Bend, United States.
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14
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Fang XQ, Liu XF, Yao L, Chen CQ, Lin JF, Gu ZD, Ni PH, Zheng XM, Fan QS. Focal adhesion kinase regulates the phosphorylation protein tyrosine phosphatase-α at Tyr789 in breast cancer cells. Mol Med Rep 2015; 11:4303-8. [PMID: 25625869 DOI: 10.3892/mmr.2015.3262] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 11/07/2014] [Indexed: 11/06/2022] Open
Abstract
Protein tyrosine phosphatase (PTP)‑α regulates the phosphorylation of focal adhesion kinase (FAK), which is important in cellular signal transduction and integration of proteins. It has been demonstrated that a FAK‑Del33 mutation (deletion of exon 33; KF437463) in breast cancer tissues regulates cell migration through FAK/Src signaling activation. However, the detailed pathway for Src activation with FAK‑Del33 remains to be elucidated. The present study used a retroviral expression system to examine changes in PTPα phosphorylation affected by the FAK‑Del33 protein in breast cancer cells. Small interfering (si)RNA targeting PTPα interfered with the phosphorylation of Src. Wound‑healing and migration assays were performed to identify cell morphology and quantitative analysis was performed by examining band color depth in western blot analysis. Significant differences were observed in the phosphorylation level of PTPα at Tyr789 between the FAK‑Del33 and the wild‑type breast cancer cells, suggesting that FAK regulated the phosphorylation level of PTPα at Tyr789 in breast cancer mutant FAK‑Del33 cells. The gene expression profile with FAK siRNA did not alter the levels of phosphorylation in other mutants, including autophosphorylation disability (Y397F), ATP kinase dominant negative (K454R) and protein 4.1, ezrin, radixin, moesin domain attenuate (Δ375). FAK RNAi inhibited the activity of the FAK‑Del33 at the Src site and rescued the elevated cell migration and invasion. The present study demonstrated for the first time, to the best of our knowledge, an increase in the phosphorylation level of PTPα‑Tyr789 by its upstream activator, FAK‑Del33, leading to Src activation in certain breast cancer cells, which has significant implications for metastatic potential.
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Affiliation(s)
- Xu-Qian Fang
- Department of Clinical Laboratory, Ruijin North Hospital, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200025, P.R. China
| | - Xiang-Fan Liu
- Faculty of Medical Laboratory Science, Shanghai JiaoTong University School of Medicine, Shanghai 200025, P.R. China
| | - Ling Yao
- Department of Biochemistry and Molecular Biology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, P.R. China
| | - Chang-Qiang Chen
- Department of Clinical Laboratory, Ruijin North Hospital, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200025, P.R. China
| | - Jia-Fei Lin
- Department of Clinical Laboratory, Ruijin North Hospital, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200025, P.R. China
| | - Zhi-Dong Gu
- Department of Clinical Laboratory, Ruijin North Hospital, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200025, P.R. China
| | - Pei-Hua Ni
- Faculty of Medical Laboratory Science, Shanghai JiaoTong University School of Medicine, Shanghai 200025, P.R. China
| | - Xin-Min Zheng
- Department of Biochemistry and Molecular Biology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, P.R. China
| | - Qi-Shi Fan
- Department of Clinical Laboratory, Ruijin North Hospital, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200025, P.R. China
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15
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Zimmer AS, Steeg PS. Meaningful prevention of breast cancer metastasis: candidate therapeutics, preclinical validation, and clinical trial concerns. J Mol Med (Berl) 2015; 93:13-29. [PMID: 25412774 PMCID: PMC6545582 DOI: 10.1007/s00109-014-1226-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 10/08/2014] [Accepted: 10/30/2014] [Indexed: 12/31/2022]
Abstract
The development of drugs to treat breast and other cancers proceeds through phase I dose finding, phase II efficacy, and phase III comparative studies in the metastatic setting, only then asking if metastasis can be prevented in adjuvant trials. Compounds without overt cytotoxic activity, such as those developed to inhibit metastatic colonization, will likely fail to shrink established lesions in the metastatic setting and never be tested in a metastasis prevention scenario where they were preclinically validated. We and others have proposed phase II primary and secondary metastasis prevention studies to address this need. Herein, we have asked whether preclinical metastasis prevention data agrees with the positive adjuvant setting trials. The data are limited but complimentary. We also review fundamental pathways involved in metastasis, including Src, integrins, focal adhesion kinase (FAK), and fibrosis, for their clinical progress to date and potential for metastasis prevention. Issues of inadequate preclinical validation and clinical toxicity profiles are discussed.
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Affiliation(s)
- Alexandra S Zimmer
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA,
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16
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Yoon H, Dehart JP, Murphy JM, Lim STS. Understanding the roles of FAK in cancer: inhibitors, genetic models, and new insights. J Histochem Cytochem 2014; 63:114-28. [PMID: 25380750 DOI: 10.1369/0022155414561498] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Focal adhesion kinase (FAK) is a protein tyrosine kinase that regulates cellular adhesion, motility, proliferation and survival in various types of cells. Interestingly, FAK is activated and/or overexpressed in advanced cancers, and promotes cancer progression and metastasis. For this reason, FAK became a potential therapeutic target in cancer, and small molecule FAK inhibitors have been developed and are being tested in clinical phase trials. These inhibitors have demonstrated to be effective by inducing tumor cell apoptosis in addition to reducing metastasis and angiogenesis. Furthermore, several genetic FAK mouse models have made advancements in understanding the specific role of FAK both in tumors and in the tumor environment. In this review, we discuss FAK inhibitors as well as genetic mouse models to provide mechanistic insights into FAK signaling and its potential in cancer therapy.
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Affiliation(s)
- Hyunho Yoon
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, Alabama
| | - Joshua P Dehart
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, Alabama
| | - James M Murphy
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, Alabama
| | - Ssang-Taek Steve Lim
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, Alabama
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17
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FAK signaling in human cancer as a target for therapeutics. Pharmacol Ther 2014; 146:132-49. [PMID: 25316657 DOI: 10.1016/j.pharmthera.2014.10.001] [Citation(s) in RCA: 295] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 10/07/2014] [Indexed: 02/08/2023]
Abstract
Focal adhesion kinase (FAK) is a key regulator of growth factor receptor- and integrin-mediated signals, governing fundamental processes in normal and cancer cells through its kinase activity and scaffolding function. Increased FAK expression and activity occurs in primary and metastatic cancers of many tissue origins, and is often associated with poor clinical outcome, highlighting FAK as a potential determinant of tumor development and metastasis. Indeed, data from cell culture and animal models of cancer provide strong lines of evidence that FAK promotes malignancy by regulating tumorigenic and metastatic potential through highly-coordinated signaling networks that orchestrate a diverse range of cellular processes, such as cell survival, proliferation, migration, invasion, epithelial-mesenchymal transition, angiogenesis and regulation of cancer stem cell activities. Such an integral role in governing malignant characteristics indicates that FAK represents a potential target for cancer therapeutics. While pharmacologic targeting of FAK scaffold function is still at an early stage of development, a number of small molecule-based FAK tyrosine kinase inhibitors are currently undergoing pre-clinical and clinical testing. In particular, PF-00562271, VS-4718 and VS-6063 show promising clinical activities in patients with selected solid cancers. Clinical testing of rationally designed FAK-targeting agents with implementation of predictive response biomarkers, such as merlin deficiency for VS-4718 in mesothelioma, may help improve clinical outcome for cancer patients. In this article, we have reviewed the current knowledge regarding FAK signaling in human cancer, and recent developments in the generation and clinical application of FAK-targeting pharmacologic agents.
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18
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Fang X, Liu X, Yao L, Chen C, Lin J, Ni P, Zheng X, Fan Q. New insights into FAK phosphorylation based on a FAT domain-defective mutation. PLoS One 2014; 9:e107134. [PMID: 25226367 PMCID: PMC4166415 DOI: 10.1371/journal.pone.0107134] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 08/11/2014] [Indexed: 01/27/2023] Open
Abstract
Mounting evidence suggests that the FAK N-terminal (FERM) domain controls FAK phosphorylation and function; however, little is known regarding the role of the C terminal (FAT) domain in FAK regulation. We identified a patient-derived FAK mutant, in which a 27-amino acid segment was deleted from the C-terminal FAT domain (named FAK-Del33). When FAK-Del33 was overexpressed in specific tumor cell lines, Y397 phosphorylation increased compared with that observed in cells expressing FAK-WT. Here, we attempt to unveil the mechanism of this increased phosphorylation. Using cell biology experiments, we show that FAK-Del33 is incapable of co-localizing with paxillin, and has constitutively high Y397 phosphorylation. With a kinase-dead mutation, it showed phosphorylation of FAK-Del33 has enhanced through auto-phosphorylation. It was also demonstrated that phosphorylation of FAK-Del33 is not Src dependent or enhanced intermolecular interactions, and that the hyperphosphorylation can be lowered using increasing amounts of transfected FERM domain. This result suggests that Del33 mutation disrupting of FAT's structural integrity and paxillin binding capacity leads to incapable of targeting Focal adhesions, but has gained the capacity for auto-phosphorylation in cis.
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Affiliation(s)
- Xuqian Fang
- Department of Clinical Laboratory, Ruijin North Hospital, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P. R. China
| | - Xiangfan Liu
- Faculty of Medical Laboratory Science, Shanghai JiaoTong University School of Medicine, Shanghai, P. R. China
| | - Ling Yao
- Department of Biochemistry and Molecular Biology, Shanghai JiaoTong University School of Medicine, Shanghai, P. R. China
| | - Changqiang Chen
- Department of Clinical Laboratory, Ruijin North Hospital, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P. R. China
| | - Jiafei Lin
- Department of Clinical Laboratory, Ruijin North Hospital, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P. R. China
| | - Peihua Ni
- Faculty of Medical Laboratory Science, Shanghai JiaoTong University School of Medicine, Shanghai, P. R. China
| | - Xinmin Zheng
- Department of Biochemistry and Molecular Biology, Shanghai JiaoTong University School of Medicine, Shanghai, P. R. China
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Qishi Fan
- Department of Clinical Laboratory, Ruijin North Hospital, Ruijin Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P. R. China
- * E-mail:
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Abstract
Focal adhesion kinase (FAK) is a cytoplasmic protein tyrosine kinase that is overexpressed and activated in several advanced-stage solid cancers. FAK promotes tumour progression and metastasis through effects on cancer cells, as well as stromal cells of the tumour microenvironment. The kinase-dependent and kinase-independent functions of FAK control cell movement, invasion, survival, gene expression and cancer stem cell self-renewal. Small molecule FAK inhibitors decrease tumour growth and metastasis in several preclinical models and have initial clinical activity in patients with limited adverse events. In this Review, we discuss FAK signalling effects on both tumour and stromal cell biology that provide rationale and support for future therapeutic opportunities.
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Affiliation(s)
- Florian J. Sulzmaier
- Department of Reproductive Medicine, UCSD Moores Cancer Center, La Jolla, CA 92093
| | - Christine Jean
- Department of Reproductive Medicine, UCSD Moores Cancer Center, La Jolla, CA 92093
| | - David D. Schlaepfer
- Department of Reproductive Medicine, UCSD Moores Cancer Center, La Jolla, CA 92093
- Address correspondence to: David D. Schlaepfer, Ph.D., University of California San Diego, Moores Cancer Center, Department of Reproductive Medicine, 3855 Health Sciences Dr., MC0803, La Jolla, CA 92093,
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