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Zeng Z, Zhu Q. Progress and prospects of biomarker-based targeted therapy and immune checkpoint inhibitors in advanced gastric cancer. Front Oncol 2024; 14:1382183. [PMID: 38947886 PMCID: PMC11211377 DOI: 10.3389/fonc.2024.1382183] [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: 02/05/2024] [Accepted: 05/24/2024] [Indexed: 07/02/2024] Open
Abstract
Gastric cancer and gastroesophageal junction cancer represent the leading cause of tumor-related death worldwide. Although advances in immunotherapy and molecular targeted therapy have expanded treatment options, they have not significantly altered the prognosis for patients with unresectable or metastatic gastric cancer. A minority of patients, particularly those with PD-L1-positive, HER-2-positive, or MSI-high tumors, may benefit more from immune checkpoint inhibitors and/or HER-2-directed therapies in advanced stages. However, for those lacking specific targets and unique molecular features, conventional chemotherapy remains the only recommended effective and durable regimen. In this review, we summarize the roles of various signaling pathways and further investigate the available targets. Then, the current results of phase II/III clinical trials in advanced gastric cancer, along with the superiorities and limitations of the existing biomarkers, are specifically discussed. Finally, we will offer our insights in precision treatment pattern when encountering the substantial challenges.
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Affiliation(s)
| | - Qing Zhu
- Department of Abdominal Oncology, West China Hospital, Sichuan University, Chengdu, China
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2
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Eckstein OS, Allen CE, Williams PM, Roy-Chowdhuri S, Patton DR, Coffey B, Reid JM, Piao J, Saguilig L, Alonzo TA, Berg SL, Ramirez NC, Jaju A, Mhlanga J, Fox E, Hawkins DS, Mooney MM, Takebe N, Tricoli JV, Janeway KA, Seibel NL, Parsons DW. Phase II Study of Selumetinib in Children and Young Adults With Tumors Harboring Activating Mitogen-Activated Protein Kinase Pathway Genetic Alterations: Arm E of the NCI-COG Pediatric MATCH Trial. J Clin Oncol 2022; 40:2235-2245. [PMID: 35363510 PMCID: PMC9273373 DOI: 10.1200/jco.21.02840] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
PURPOSE The NCI-COG Pediatric MATCH trial assigns patients age 1-21 years with relapsed or refractory solid tumors, lymphomas, and histiocytic disorders to phase II studies of molecularly targeted therapies on the basis of detection of predefined genetic alterations. Patients with tumors harboring mutations or fusions driving activation of the mitogen-activated protein kinase (MAPK) pathway were treated with the MEK inhibitor selumetinib. METHODS Patients received selumetinib twice daily for 28-day cycles until disease progression or intolerable toxicity. The primary end point was objective response rate; secondary end points included progression-free survival and tolerability of selumetinib. RESULTS Twenty patients (median age: 14 years) were treated. All were evaluable for response and toxicities. The most frequent diagnoses were high-grade glioma (HGG; n = 7) and rhabdomyosarcoma (n = 7). Twenty-one actionable mutations were detected: hotspot mutations in KRAS (n = 8), NRAS (n = 3), and HRAS (n = 1), inactivating mutations in NF1 (n = 7), and BRAF V600E (n = 2). No objective responses were observed. Three patients had a best response of stable disease including two patients with HGG (NF1 mutation, six cycles; KRAS mutation, 12 cycles). Six-month progression-free survival was 15% (95% CI, 4 to 34). Five patients (25%) experienced a grade 3 or higher adverse event that was possibly or probably attributable to study drug. CONCLUSION A national histology-agnostic molecular screening strategy was effective at identifying children and young adults eligible for treatment with selumetinib in the first Pediatric MATCH treatment arm to be completed. MEK inhibitors have demonstrated promising responses in some pediatric tumors (eg, low-grade glioma and plexiform neurofibroma). However, selumetinib in this cohort with treatment-refractory tumors harboring MAPK alterations demonstrated limited efficacy, indicating that pathway mutation status alone is insufficient to predict response to selumetinib monotherapy for pediatric cancers.
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Affiliation(s)
- Olive S. Eckstein
- Texas Children's Cancer and Hematology Centers, Baylor College of Medicine, Houston, TX
| | - Carl E. Allen
- Texas Children's Cancer and Hematology Centers, Baylor College of Medicine, Houston, TX,Carl E. Allen, MD, PhD, Texas Children's Cancer and Hematology Centers, Baylor College of Medicine, 1102 Bates Ave, Suite 1025, Houston, TX 77030; e-mail:
| | | | | | - David R. Patton
- Center for Biomedical Informatics and Information Technology, NCI, NIH, Bethesda, MD
| | - Brent Coffey
- Center for Biomedical Informatics and Information Technology, NCI, NIH, Bethesda, MD
| | | | - Jin Piao
- Keck School of Medicine, University of Southern California, Los Angeles, CA
| | | | - Todd A. Alonzo
- Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Stacey L. Berg
- Texas Children's Cancer and Hematology Centers, Baylor College of Medicine, Houston, TX
| | - Nilsa C. Ramirez
- Biopathology Center, Research Institute at Nationwide Children's Hospital, Columbus, OH
| | - Alok Jaju
- Ann and Robert H. Lurie Children's Hospital, Chicago, IL
| | - Joyce Mhlanga
- Washington University School of Medicine, St Louis, MO
| | | | | | - Margaret M. Mooney
- Division of Cancer Treatment and Diagnosis, Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD
| | - Naoko Takebe
- Division of Cancer Treatment and Diagnosis, Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD
| | - James V. Tricoli
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD
| | | | - Nita L. Seibel
- Division of Cancer Treatment and Diagnosis, Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD
| | - D. Williams Parsons
- Texas Children's Cancer and Hematology Centers, Baylor College of Medicine, Houston, TX
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3
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BRAF Modulates Lipid Use and Accumulation. Cancers (Basel) 2022; 14:cancers14092110. [PMID: 35565240 PMCID: PMC9105200 DOI: 10.3390/cancers14092110] [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: 03/23/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 12/24/2022] Open
Abstract
There is increasing evidence that oxidative metabolism and fatty acids play an important role in BRAF-driven tumorigenesis, yet the effect of BRAF mutation and expression on metabolism is poorly understood. We examined how BRAF mutation and expression modulates metabolite abundance. Using the non-transformed NIH3T3 cell line, we generated cells that stably overexpressed BRAF V600E or BRAF WT. We found that cells expressing BRAF V600E were enriched with immunomodulatory lipids. Further, we found a unique transcriptional signature that was exclusive to BRAF V600E expression. We also report that BRAF V600E mutation promoted accumulation of long chain polyunsaturated fatty acids (PUFAs) and rewired metabolic flux for non-Warburg behavior. This cancer promoting mutation further induced the formation of tunneling nanotube (TNT)-like protrusions in NIH3T3 cells that preferentially accumulated lipid droplets. In the plasma of melanoma patients harboring the BRAF V600E mutation, levels of lysophosphatidic acid, sphingomyelin, and long chain fatty acids were significantly increased in the cohort of patients that did not respond to BRAF inhibitor therapy. Our findings show BRAF V600 status plays an important role in regulating immunomodulatory lipid profiles and lipid trafficking, which may inform future therapy across cancers.
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Lin YF, Liu JJ, Chang YJ, Yu CS, Yi W, Lane HY, Lu CH. Predicting Anticancer Drug Resistance Mediated by Mutations. Pharmaceuticals (Basel) 2022; 15:ph15020136. [PMID: 35215249 PMCID: PMC8878306 DOI: 10.3390/ph15020136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/16/2022] [Accepted: 01/21/2022] [Indexed: 02/01/2023] Open
Abstract
Cancer drug resistance presents a challenge for precision medicine. Drug-resistant mutations are always emerging. In this study, we explored the relationship between drug-resistant mutations and drug resistance from the perspective of protein structure. By combining data from previously identified drug-resistant mutations and information of protein structure and function, we used machine learning-based methods to build models to predict cancer drug resistance mutations. The performance of our combined model achieved an accuracy of 86%, a Matthews correlation coefficient score of 0.57, and an F1 score of 0.66. We have constructed a fast, reliable method that predicts and investigates cancer drug resistance in a protein structure. Nonetheless, more information is needed concerning drug resistance and, in particular, clarification is needed about the relationships between the drug and the drug resistance mutations in proteins. Highly accurate predictions regarding drug resistance mutations can be helpful for developing new strategies with personalized cancer treatments. Our novel concept, which combines protein structure information, has the potential to elucidate physiological mechanisms of cancer drug resistance.
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Affiliation(s)
- Yu-Feng Lin
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung 41354, Taiwan; (Y.-F.L.); (W.Y.)
| | - Jia-Jun Liu
- The Ph.D. Program of Biotechnology and Biomedical Industry, China Medical University, Taichung 40402, Taiwan; (J.-J.L.); (Y.-J.C.)
| | - Yu-Jen Chang
- The Ph.D. Program of Biotechnology and Biomedical Industry, China Medical University, Taichung 40402, Taiwan; (J.-J.L.); (Y.-J.C.)
| | - Chin-Sheng Yu
- Department of Information Engineering and Computer Science, Feng Chia University, Taichung 40201, Taiwan;
| | - Wei Yi
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung 41354, Taiwan; (Y.-F.L.); (W.Y.)
| | - Hsien-Yuan Lane
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 40402, Taiwan;
- Department of Psychiatry, China Medical University Hospital, Taichung 40402, Taiwan
- Brain Disease Research Center, China Medical University Hospital, Taichung 40402, Taiwan
| | - Chih-Hao Lu
- The Ph.D. Program of Biotechnology and Biomedical Industry, China Medical University, Taichung 40402, Taiwan; (J.-J.L.); (Y.-J.C.)
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 40402, Taiwan;
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 40402, Taiwan
- Correspondence:
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5
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Guimarães LM, Coura BP, Gomez RS, Gomes CC. The Molecular Pathology of Odontogenic Tumors: Expanding the Spectrum of MAPK Pathway Driven Tumors. FRONTIERS IN ORAL HEALTH 2022; 2:740788. [PMID: 35048058 PMCID: PMC8757814 DOI: 10.3389/froh.2021.740788] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/13/2021] [Indexed: 12/13/2022] Open
Abstract
Odontogenic tumors comprise a heterogeneous group of lesions that arise from the odontogenic apparatus and their remnants. Although the etiopathogenesis of most odontogenic tumors remains unclear, there have been some advances, recently, in the understanding of the genetic basis of specific odontogenic tumors. The mitogen-activated protein kinases/extracellular signal-regulated kinases (MAPK/ERK) pathway is intimately involved in the regulation of important cellular functions, and it is commonly deregulated in several human neoplasms. Molecular analysis performed by different techniques, including direct sequencing, next-generation sequencing, and allele-specific qPCR, have uncovered mutations in genes related to the oncogenic MAPK/ERK signaling pathway in odontogenic tumors. Genetic mutations in this pathway genes have been reported in epithelial and mixed odontogenic tumors, in addition to odontogenic carcinomas and sarcomas. Notably, B-Raf proto-oncogene serine/threonine kinase (BRAF) and KRAS proto-oncogene GTPase (KRAS) pathogenic mutations have been reported in a high proportion of ameloblastomas and adenomatoid odontogenic tumors, respectively. In line with the reports about other neoplasms that harbor a malignant counterpart, the frequency of BRAF p.V600E mutation is higher in ameloblastoma (64% in conventional, 81% in unicystic, and 63% in peripheral) than in ameloblastic carcinoma (35%). The objective of this study was to review MAPK/ERK genetic mutations in benign and malignant odontogenic tumors. Additionally, such genetic alterations were discussed in the context of tumorigenesis, clinical behavior, classification, and future perspectives regarding therapeutic approaches.
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Affiliation(s)
- Letícia Martins Guimarães
- Department of Pathology, Biological Sciences Institute, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Bruna Pizziolo Coura
- Department of Pathology, Biological Sciences Institute, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ricardo Santiago Gomez
- Department of Oral Surgery and Pathology, Faculty of Dentistry, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Carolina Cavalieri Gomes
- Department of Pathology, Biological Sciences Institute, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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S L, A S, Dv S, Bs R, R S, Sharaf S, Sa A, G R. Comparative differential cytotoxicity of clinically used SERMs in human cancer lines of different origin and its predictive molecular docking studies of key target genes involved in cancer progression and treatment responses. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2021; 3:100080. [PMID: 35059624 PMCID: PMC8760488 DOI: 10.1016/j.crphar.2021.100080] [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: 08/06/2021] [Revised: 12/18/2021] [Accepted: 12/21/2021] [Indexed: 12/24/2022] Open
Abstract
SERMS like Tamoxifene, 5-hydroxy tamoxifene, raloxifene and endoxifene has been used for the treatment of hormonal imbalances and dependent cancers owing to their action via Estrogen receptors as in the treatment of estrogen sensitive breast cancers. Due to the adverse side effects, modifications and development of the existing or newer SERMS has always been of immense interest. Ormeloxifene, a SERM molecule manufactured by HLL Lifecare Ltd, India as birth control under the trade names Saheli, Novex, and Novex-DS which is also investigated against mastalgia, fibro-adenoma and abnormal uterine bleeding. Anti-cancer effects have been reported in estrogen dependent and independent cancers which shows its wide scope to be implemented in cancer therapy. Current investigation is a comprehensive effort to find the cytotoxic potential of Ormeloxifene in comparison with clinically used four SERMS in twenty six cancer cell lines of different origin using Adriamycin as positive control. Also the computational studies pertaining to selected target/ligand with respect to tumor progression, development, treatment responses and apoptosis. The studies proved effective cytotoxicity of Ormeloxifene on cancer cell lines with lower TGI, GI50 and LC50 values which are significantly comparable. Also the in silico studies proved that the docking score of the compound suggests the interaction of the compound which could tightly regulate key target genes controlling cancer like ER, EGFR kinase, EGFR-cSRC, HDAC-2, PARP-1 and BRAF. This study brings out the superior efficacy of Ormeloxifene compared to other SERMS with proven safety profile to be repositioned as an anti-cancer drug to treat diverse cancer types.
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Affiliation(s)
- Lakshmi S
- Corporate R&D Centre, HLL Lifecare Limited, Thiruvananthapuram, Pincode- 695 017, India
| | - Shanitha A
- Dept. of Computational Biology & Bioinformatics, University of Kerala, Thiruvananthapuram, Pincode-695581, India
| | - Shiny Dv
- Corporate R&D Centre, HLL Lifecare Limited, Thiruvananthapuram, Pincode- 695 017, India
| | - Rahul Bs
- Corporate R&D Centre, HLL Lifecare Limited, Thiruvananthapuram, Pincode- 695 017, India
| | - Saikant R
- Corporate R&D Centre, HLL Lifecare Limited, Thiruvananthapuram, Pincode- 695 017, India
| | - Shehna Sharaf
- Corporate R&D Centre, HLL Lifecare Limited, Thiruvananthapuram, Pincode- 695 017, India
| | - Abi Sa
- Corporate R&D Centre, HLL Lifecare Limited, Thiruvananthapuram, Pincode- 695 017, India
| | - Rajmohan G
- Corporate R&D Centre, HLL Lifecare Limited, Thiruvananthapuram, Pincode- 695 017, India
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7
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Panagopoulos I, Heim S. Interstitial Deletions Generating Fusion Genes. Cancer Genomics Proteomics 2021; 18:167-196. [PMID: 33893073 DOI: 10.21873/cgp.20251] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 12/16/2022] Open
Abstract
A fusion gene is the physical juxtaposition of two different genes resulting in a structure consisting of the head of one gene and the tail of the other. Gene fusion is often a primary neoplasia-inducing event in leukemias, lymphomas, solid malignancies as well as benign tumors. Knowledge about fusion genes is crucial not only for our understanding of tumorigenesis, but also for the diagnosis, prognostication, and treatment of cancer. Balanced chromosomal rearrangements, in particular translocations and inversions, are the most frequent genetic events leading to the generation of fusion genes. In the present review, we summarize the existing knowledge on chromosome deletions as a mechanism for fusion gene formation. Such deletions are mostly submicroscopic and, hence, not detected by cytogenetic analyses but by array comparative genome hybridization (aCGH) and/or high throughput sequencing (HTS). They are found across the genome in a variety of neoplasias. As tumors are increasingly analyzed using aCGH and HTS, it is likely that more interstitial deletions giving rise to fusion genes will be found, significantly impacting our understanding and treatment of cancer.
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Affiliation(s)
- Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway;
| | - Sverre Heim
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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8
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Han J, Jung Y, Jun Y, Park S, Lee S. Elucidating molecular mechanisms of acquired resistance to BRAF inhibitors in melanoma using a microfluidic device and deep sequencing. Genomics Inform 2021; 19:e2. [PMID: 33840166 PMCID: PMC8042304 DOI: 10.5808/gi.20074] [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: 12/11/2020] [Revised: 01/09/2021] [Accepted: 01/15/2021] [Indexed: 12/01/2022] Open
Abstract
BRAF inhibitors (e.g., vemurafenib) are widely used to treat metastatic melanoma with the BRAF V600E mutation. The initial response is often dramatic, but treatment resistance leads to disease progression in the majority of cases. Although secondary mutations in the mitogen-activated protein kinase signaling pathway are known to be responsible for this phenomenon, the molecular mechanisms governing acquired resistance are not known in more than half of patients. Here we report a genome- and transcriptome-wide study investigating the molecular mechanisms of acquired resistance to BRAF inhibitors. A microfluidic chip with a concentration gradient of vemurafenib was utilized to rapidly obtain therapy-resistant clones from two melanoma cell lines with the BRAF V600E mutation (A375 and SK-MEL-28). Exome and transcriptome data were produced from 13 resistant clones and analyzed to identify secondary mutations and gene expression changes. Various mechanisms, including phenotype switching and metabolic reprogramming, have been determined to contribute to resistance development differently for each clone. The roles of microphthalmia-associated transcription factor, the master transcription factor in melanocyte differentiation/dedifferentiation, were highlighted in terms of phenotype switching. Our study provides an omics-based comprehensive overview of the molecular mechanisms governing acquired resistance to BRAF inhibitor therapy.
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Affiliation(s)
- Jiyeon Han
- Department of Bio-information Science, Ewha Womans University, Seoul 03760, Korea
| | - Yeonjoo Jung
- Ewha Research Center for Systems Biology (ERCSB), Ewha Womans University, Seoul 03760, Korea
| | - Yukyung Jun
- Ewha Research Center for Systems Biology (ERCSB), Ewha Womans University, Seoul 03760, Korea
| | - Sungsu Park
- Center for Supercomputing Application, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon 34141, Korea
| | - Sanghyuk Lee
- Department of Bio-information Science, Ewha Womans University, Seoul 03760, Korea
- Ewha Research Center for Systems Biology (ERCSB), Ewha Womans University, Seoul 03760, Korea
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Goh CJH, Wong JH, El Farran C, Tan BX, Coffill CR, Loh YH, Lane D, Arumugam P. Identification of pathways modulating vemurafenib resistance in melanoma cells via a genome-wide CRISPR/Cas9 screen. G3 (BETHESDA, MD.) 2021; 11:jkaa069. [PMID: 33604667 PMCID: PMC8022920 DOI: 10.1093/g3journal/jkaa069] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/08/2020] [Indexed: 12/15/2022]
Abstract
Vemurafenib is a BRAF kinase inhibitor (BRAFi) that is used to treat melanoma patients harboring the constitutively active BRAF-V600E mutation. However, after a few months of treatment patients often develop resistance to vemurafenib leading to disease progression. Sequence analysis of drug-resistant tumor cells and functional genomic screens has identified several genes that regulate vemurafenib resistance. Reactivation of mitogen-activated protein kinase (MAPK) pathway is a recurrent feature of cells that develop resistance to vemurafenib. We performed a genome-scale CRISPR-based knockout screen to identify modulators of vemurafenib resistance in melanoma cells with a highly improved CRISPR sgRNA library called Brunello. We identified 33 genes that regulate resistance to vemurafenib out of which 14 genes have not been reported before. Gene ontology enrichment analysis showed that the hit genes regulate histone modification, transcription and cell cycle. We discuss how inactivation of hit genes might confer resistance to vemurafenib and provide a framework for follow-up investigations.
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Affiliation(s)
| | - Jin Huei Wong
- Bioinformatics Institute (BII), A*STAR, Singapore 138671, Singapore
| | - Chadi El Farran
- Epigenetics and Cell Fates Laboratory, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
| | - Ban Xiong Tan
- Experimental Drug Development Centre, A*STAR, Singapore 138670, Singapore
| | | | - Yuin-Hain Loh
- Epigenetics and Cell Fates Laboratory, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
| | - David Lane
- p53Lab, A*STAR, Singapore 138648, Singapore
| | - Prakash Arumugam
- Bioinformatics Institute (BII), A*STAR, Singapore 138671, Singapore
- Singapore Institute for Food and Biotechnology Innovation, Singapore 138632, Singapore
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Peng D, Li H, Hu B, Zhang H, Chen L, Lin S, Zuo Z, Xue Y, Ren J, Xie Y. PTMsnp: A Web Server for the Identification of Driver Mutations That Affect Protein Post-translational Modification. Front Cell Dev Biol 2020; 8:593661. [PMID: 33240890 PMCID: PMC7683509 DOI: 10.3389/fcell.2020.593661] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/21/2020] [Indexed: 11/16/2022] Open
Abstract
High-throughput sequencing technologies have identified millions of genetic mutations in multiple human diseases. However, the interpretation of the pathogenesis of these mutations and the discovery of driver genes that dominate disease progression is still a major challenge. Combining functional features such as protein post-translational modification (PTM) with genetic mutations is an effective way to predict such alterations. Here, we present PTMsnp, a web server that implements a Bayesian hierarchical model to identify driver genetic mutations targeting PTM sites. PTMsnp accepts genetic mutations in a standard variant call format or tabular format as input and outputs several interactive charts of PTM-related mutations that potentially affect PTMs. Additional functional annotations are performed to evaluate the impact of PTM-related mutations on protein structure and function, as well as to classify variants relevant to Mendelian disease. A total of 4,11,574 modification sites from 33 different types of PTMs and 1,776,848 somatic mutations from TCGA across 33 different cancer types are integrated into the web server, enabling identification of candidate cancer driver genes based on PTM. Applications of PTMsnp to the cancer cohorts and a GWAS dataset of type 2 diabetes identified a set of potential drivers together with several known disease-related genes, indicating its reliability in distinguishing disease-related mutations and providing potential molecular targets for new therapeutic strategies. PTMsnp is freely available at: http://ptmsnp.renlab.org.
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Affiliation(s)
- Di Peng
- Precision Medicine Institute, The First Affiliated Hospital, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Huiqin Li
- Precision Medicine Institute, The First Affiliated Hospital, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Bosu Hu
- Precision Medicine Institute, The First Affiliated Hospital, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hongwan Zhang
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, China
| | - Li Chen
- Precision Medicine Institute, The First Affiliated Hospital, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shaofeng Lin
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Zhixiang Zuo
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yu Xue
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jian Ren
- Precision Medicine Institute, The First Affiliated Hospital, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yubin Xie
- Precision Medicine Institute, The First Affiliated Hospital, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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11
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Menezes R, Foito A, Jardim C, Costa I, Garcia G, Rosado-Ramos R, Freitag S, Alexander CJ, Outeiro TF, Stewart D, Santos CN. Bioprospection of Natural Sources of Polyphenols with Therapeutic Potential for Redox-Related Diseases. Antioxidants (Basel) 2020; 9:antiox9090789. [PMID: 32858836 PMCID: PMC7576474 DOI: 10.3390/antiox9090789] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/14/2020] [Accepted: 08/18/2020] [Indexed: 12/23/2022] Open
Abstract
Plants are a reservoir of high-value molecules with underexplored biomedical applications. With the aim of identifying novel health-promoting attributes in underexplored natural sources, we scrutinized the diversity of (poly)phenols present within the berries of selected germplasm from cultivated, wild, and underutilized Rubus species. Our strategy combined the application of metabolomics, statistical analysis, and evaluation of (poly)phenols' bioactivity using a yeast-based discovery platform. We identified species as sources of (poly)phenols interfering with pathological processes associated with redox-related diseases, particularly, amyotrophic lateral sclerosis, cancer, and inflammation. In silico prediction of putative bioactives suggested cyanidin-hexoside as an anti-inflammatory molecule which was validated in yeast and mammalian cells. Moreover, cellular assays revealed that the cyanidin moiety was responsible for the anti-inflammatory properties of cyanidin-hexoside. Our findings unveiled novel (poly)phenolic bioactivities and illustrated the power of our integrative approach for the identification of dietary (poly)phenols with potential biomedical applications.
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Affiliation(s)
- Regina Menezes
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School/Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal; (R.M.); (R.R.-R.)
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (C.J.); (I.C.); (G.G.)
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Alexandre Foito
- Environmental and Biochemical Science Group, The James Hutton Institute, Dundee DD2 5DA, UK; (A.F.); (S.F.); (D.S.)
| | - Carolina Jardim
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (C.J.); (I.C.); (G.G.)
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Inês Costa
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (C.J.); (I.C.); (G.G.)
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Gonçalo Garcia
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (C.J.); (I.C.); (G.G.)
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Rita Rosado-Ramos
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School/Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal; (R.M.); (R.R.-R.)
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (C.J.); (I.C.); (G.G.)
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Sabine Freitag
- Environmental and Biochemical Science Group, The James Hutton Institute, Dundee DD2 5DA, UK; (A.F.); (S.F.); (D.S.)
| | | | - Tiago Fleming Outeiro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Goettinge, 37073 Göttingen, Germany;
- Max Planck Institute for Experimental Medicine, 37075 Göttingen, Germany
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne NE2 4HH, UK
| | - Derek Stewart
- Environmental and Biochemical Science Group, The James Hutton Institute, Dundee DD2 5DA, UK; (A.F.); (S.F.); (D.S.)
- School of Engineering and Physical Sciences, Institute of Mechanical, Process and Energy Engineering, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Cláudia N. Santos
- CEDOC, Chronic Diseases Research Centre, NOVA Medical School/Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal; (R.M.); (R.R.-R.)
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; (C.J.); (I.C.); (G.G.)
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
- Correspondence:
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12
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Calvete O, Garcia-Pavia P, Domínguez F, Mosteiro L, Pérez-Cabornero L, Cantalapiedra D, Zorio E, Ramón Y Cajal T, Crespo-Leiro MG, Teulé Á, Lázaro C, Morente MM, Urioste M, Benitez J. POT1 and Damage Response Malfunction Trigger Acquisition of Somatic Activating Mutations in the VEGF Pathway in Cardiac Angiosarcomas. J Am Heart Assoc 2019; 8:e012875. [PMID: 31510873 PMCID: PMC6818007 DOI: 10.1161/jaha.119.012875] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Background Mutations in the POT1 gene explain abnormally long telomeres and multiple tumors including cardiac angiosarcomas (CAS). However, the link between long telomeres and tumorigenesis is poorly understood. Methods and Results Here, we have studied the somatic landscape of 3 different angiosarcoma patients with mutations in the POT1 gene to further investigate this tumorigenesis process. In addition, the genetic landscape of 7 CAS patients without mutations in the POT1 gene has been studied. Patients with CAS and nonfunctional POT1 did not repress ATR (ataxia telangiectasia RAD3-related)-dependent DNA damage signaling and showed a constitutive increase of cell cycle arrest and somatic activating mutations in the VEGF (vascular endothelial growth factor)/angiogenesis pathway (KDR gene). The same observation was made in POT1 mutation carriers with tumors different from CAS and also in CAS patients without mutations in the POT1 gene but with mutations in other genes involved in DNA damage signaling. Conclusions Inhibition of POT1 function and damage-response malfunction activated DNA damage signaling and increased cell cycle arrest as well as interfered with apoptosis, which would permit acquisition of somatic mutations in the VEGF/angiogenesis pathway that drives tumor formation. Therapies based on the inhibition of damage signaling in asymptomatic carriers may diminish defects on cell cycle arrest and thus prevent the apoptosis deregulation that leads to the acquisition of driver mutations.
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Affiliation(s)
- Oriol Calvete
- Human Genetics Group Spanish National Cancer Research Center (CNIO) Madrid Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER) Madrid Spain
| | - Pablo Garcia-Pavia
- Department of Cardiology Hospital Universitario Puerta de Hierro Madrid Spain.,Center for Biomedical Network Research on Cardiovascular Diseases (CIBERCV) Madrid Spain.,Facultad de Ciencias de la Salud Universidad Francisco de Vitoria (UFV) Madrid Spain
| | - Fernando Domínguez
- Department of Cardiology Hospital Universitario Puerta de Hierro Madrid Spain.,Center for Biomedical Network Research on Cardiovascular Diseases (CIBERCV) Madrid Spain.,Spanish National Cardiovascular Research Center (CNIC) Madrid Spain
| | - Lluc Mosteiro
- Tumour Suppression Group Spanish National Cancer Research Center (CNIO) Madrid Spain
| | - Lucía Pérez-Cabornero
- Medical Genetics Unit Sistemas Genómicos Parque Tecnológico de Valencia Paterna Spain
| | - Diego Cantalapiedra
- Medical Genetics Unit Sistemas Genómicos Parque Tecnológico de Valencia Paterna Spain
| | - Esther Zorio
- Department of Cardiology Hospital Universitario y Politécnico La Fe Valencia Spain
| | | | - Maria G Crespo-Leiro
- Department of Cardiology Hospital Universitario Puerta de Hierro Madrid Spain.,Department of Cardiology Instituto de Investigación Biomédica de A Coruña (INIBIC) Complexo Hospitalario Universitario de A Coruña (CHUfSiAC) A Coruña Spain
| | - Álex Teulé
- Hereditary Cancer Program-Medical Oncology Service Catalan Institute of Oncology ICO-IDIBELL and CIBERONC Barcelona Spain
| | - Conxi Lázaro
- Medical Oncology Service Catalan Institute of Oncology ICO-IDIBELL and CIBERONC Barcelona Spain
| | - Manuel M Morente
- Biobank Unit Spanish National Cancer Research Center (CNIO) Madrid Spain
| | - Miguel Urioste
- Center for Biomedical Network Research on Rare Diseases (CIBERER) Madrid Spain.,Familial Cancer Clinical Unit Spanish National Cancer Research Center (CNIO) Madrid Spain
| | - Javier Benitez
- Human Genetics Group Spanish National Cancer Research Center (CNIO) Madrid Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER) Madrid Spain
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13
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Auliac JB, Bayle S, Vergnenegre A, Le Caer H, Falchero L, Gervais R, Doubre H, Vinas F, Marin B, Chouaid C. Patients with non-small-cell lung cancer harbouring a BRAF mutation: a multicentre study exploring clinical characteristics, management, and outcomes in a real-life setting: EXPLORE GFPC 02-14. ACTA ACUST UNITED AC 2018; 25:e398-e402. [PMID: 30464690 DOI: 10.3747/co.25.3945] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Background Mutations in BRAF are rare oncogene mutations, found in 2% of non-small-cell lung cancers (nsclcs). Little information is available about the management of patients with BRAF-mutated nsclc, except for those included in clinical trials. We undertook the present study to assess the clinical characteristics, management, and outcomes of those patients in a real-life setting. Methods This retrospective multicentre observational study included all patients with BRAF-mutated nsclc diagnosed between January 2012 and December 2014. Results Patients (n = 59) from 24 centres were included: 57.6% men; mean age: 64.5 ± 14.5 years; 82% with a performance status of 0-1 at diagnosis; smoking status: 40.3% current, 32.6% former; 93% with adenocarcinoma histology; 75% stage iv; 78% with V600E mutations; 2 with EGFR and 2 with ALK co-mutations. Of the stage iv patients, 79% received first-line therapy (14.2% anti-BRAF), and 48% received second-line treatment (23.8% anti-BRAF). Response rate and progression-free survival were, respectively, 51.7% and 8.7 months [95% confidence interval (ci): 6.4 months to 15.2 months] for first-line therapy and 35.3% and 4.1 months (95% ci: 2 months to 10.9 months) for second-line treatments. The 2-year overall survival was 58.5% (95% ci: 45.8% to 74.8%). Outcomes in patients with stage iv nsclc harbouring BRAF V600E mutations (n = 32) did not differ significantly from those of patients with other BRAF mutations. Conclusions In this real-world analysis, most nsclc patients with a BRAF mutation were men and current or former smokers. Survival appears to be better in these BRAF-mutated patients than in nsclc patients without an oncogenic driver.
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Affiliation(s)
- J B Auliac
- Chest Department, Hôpital François-Quesnay, Mantes-la-Jolie, France
| | - S Bayle
- Oncology Department, Institut d'Oncology, Saint-Priest-en-Jarez, France
| | | | - H Le Caer
- Chest Department, ch Saint Brieux, Saint Brieuc, France
| | - L Falchero
- Chest Department, ch Villefranche, Villefranche, France
| | - R Gervais
- Oncology Department, Centre Francois Baclesse, Caen, France
| | - H Doubre
- Chest Department, Hôpital Foch, Suresnes, France
| | - F Vinas
- Chest Department, chi Créteil, Créteil, France
| | - B Marin
- Chest Department, chu de Limoges, Limoges, France
| | - C Chouaid
- Chest Department, chi Créteil, Créteil, France
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14
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Allen CE, Laetsch TW, Mody R, Irwin MS, Lim MS, Adamson PC, Seibel NL, Parsons DW, Cho YJ, Janeway K. Target and Agent Prioritization for the Children's Oncology Group-National Cancer Institute Pediatric MATCH Trial. J Natl Cancer Inst 2017; 109:2972640. [PMID: 28376230 DOI: 10.1093/jnci/djw274] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 10/13/2016] [Indexed: 12/15/2022] Open
Abstract
Over the past decades, outcomes for children with cancer have improved dramatically through serial clinical trials based in large measure on dose intensification of cytotoxic chemotherapy for children with high-risk malignancies. Progress made through such dose intensification, in general, is no longer yielding further improvements in outcome. With the revolution in sequencing technologies and rapid development of drugs that block specific proteins and pathways, there is now an opportunity to improve outcomes for pediatric cancer patients through mutation-based targeted therapeutic strategies. The Children's Oncology Group (COG), in partnership with the National Cancer Institute (NCI), is planning a trial entitled the COG-NCI Pediatric Molecular Analysis for Therapeutic Choice (Pediatric MATCH) protocol utilizing an umbrella design. This protocol will have centralized infrastructure and will consist of a biomarker profiling protocol and multiple single-arm phase II trials of targeted therapies. Pediatric patients with recurrent or refractory solid tumors, lymphomas, or histiocytoses with measurable disease will be eligible. The Pediatric MATCH Target and Agent Prioritization (TAP) committee includes membership representing COG disease committees, the Food and Drug Administration, and the NCI. The TAP Committee systematically reviewed target and agent pairs for inclusion in the Pediatric MATCH trial. Fifteen drug-target pairs were reviewed by the TAP Committee, with seven recommended for further development as initial arms of the Pediatric MATCH trial. The current evidence for availability, efficacy, and safety of targeted agents in children for each class of mutation considered for inclusion in the Pediatric MATCH trial is discussed in this review.
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Affiliation(s)
- Carl E Allen
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX, USA.,Division of Pediatric Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Theodore W Laetsch
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Pauline Allen Gill Center for Cancer and Blood Disorders, Children's Health, Dallas, TX, USA
| | - Rajen Mody
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Meredith S Irwin
- Department of Pediatrics, Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON, Canada
| | - Megan S Lim
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Hospital of the University of Pennsylvania and Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Peter C Adamson
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nita L Seibel
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - D Williams Parsons
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX, USA.,Division of Pediatric Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Y Jae Cho
- Division of Pediatric Neurology, Doernbecher Children's Hospital, Portland, OR, USA.,Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Katherine Janeway
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer Center and Blood Disorder Center, Boston, MA, USA
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15
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Jin S, Borkhuu O, Bao W, Yang YT. Signaling Pathways in Thyroid Cancer and Their Therapeutic Implications. J Clin Med Res 2016; 8:284-96. [PMID: 26985248 PMCID: PMC4780491 DOI: 10.14740/jocmr2480w] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2016] [Indexed: 12/20/2022] Open
Abstract
Thyroid cancer is a common malignancy of endocrine system, and has now become the fastest increasing cancer among all the malignancies. The development, progression, invasion, and metastasis are closely associated with multiple signaling pathways and the functions of related molecules, such as Src, Janus kinase (JAK)-signal transducers and activators of transcription (STAT), mitogen-activated protein kinase (MAPK), phosphoinositide 3-kinase (PI3K)/Akt, NF-κB, thyroid stimulating hormone receptor (TSHR), Wnt-β-catenin and Notch signaling pathways. Each of the signaling pathways could exert its function singly or through network with other pathways. These pathways could cooperate, promote, antagonize, or interact with each other to form a complex network for the regulation. Dysfunction of this network could increase the development, progression, invasion, and metastasis of thyroid cancer. Inoperable thyroid cancer still has a poor prognosis. However, signaling pathway-related targeted therapies offer the hope of longer quality of meaningful life for this small group of patients. Signaling pathway-related targets provide unprecedented opportunities for further research and clinical development of novel treatment strategies for this cancer. In the present work, the advances in these signaling pathways and targeted treatments of thyroid cancer were reviewed.
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Affiliation(s)
- Shan Jin
- Department of General Surgery, Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, Inner Mongolia Autonomous Region, China
| | - Oyungerel Borkhuu
- Department of General Surgery, Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, Inner Mongolia Autonomous Region, China
| | - Wuyuntu Bao
- Department of General Surgery, Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, Inner Mongolia Autonomous Region, China
| | - Yun-Tian Yang
- Department of General Surgery, Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, Inner Mongolia Autonomous Region, China
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16
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Ahn JH, Han BI, Lee M. Induction of Resistance to BRAF Inhibitor Is Associated with the Inability of Spry2 to Inhibit BRAF-V600E Activity in BRAF Mutant Cells. Biomol Ther (Seoul) 2015; 23:320-6. [PMID: 26157547 PMCID: PMC4489825 DOI: 10.4062/biomolther.2015.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 04/06/2015] [Accepted: 04/08/2015] [Indexed: 12/05/2022] Open
Abstract
The clinical benefits of oncogenic BRAF inhibitor therapies are limited by the emergence of drug resistance. In this study, we investigated the role of a negative regulator of the MAPK pathway, Spry2, in acquired resistance using BRAF inhibitor-resistant derivatives of the BRAF-V600E melanoma (A375P/Mdr). Real-time RT-PCR analysis indicated that the expression of Spry2 was higher in A375P cells harboring the BRAF V600E mutation compared with wild-type BRAF-bearing cells (SK-MEL-2) that are resistant to BRAF inhibitors. This result suggests the ability of BRAF V600E to evade feedback suppression in cell lines with BRAF V600E mutations despite high Spry2 expression. Most interestingly, Spry2 exhibited strongly reduced expression in A375P/Mdr cells with acquired resistance to BRAF inhibitors. Furthermore, the overexpression of Spry2 partially restored sensitivity to the BRAF inhibitor PLX4720 in two BRAF inhibitor-resistant cells, indicating a positive role for Spry2 in the growth inhibition induced by BRAF inhibitors. On the other hand, long-term treatment with PLX4720 induced pERK reactivation following BRAF inhibition in A375P cells, indicating that negative feedback including Spry2 may be bypassed in BRAF mutant melanoma cells. In addition, the siRNA-mediated knockdown of Raf-1 attenuated the rebound activation of ERK stimulated by PLX4720 in A375P cells, strongly suggesting the positive role of Raf-1 kinase in ERK activation in response to BRAF inhibition. Taken together, these data suggest that RAF signaling may be released from negative feedback inhibition through interacting with Spry2, leading to ERK rebound and, consequently, the induction of acquired resistance to BRAF inhibitors.
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Affiliation(s)
- Jun-Ho Ahn
- Genome Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806
| | - Byeal-I Han
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 406-772, Republic of Korea
| | - Michael Lee
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 406-772, Republic of Korea
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17
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Abstract
"Langerhans cell histiocytosis" (LCH) describes a spectrum of clinical presentations ranging from a single bone lesion or trivial skin rash to an explosive disseminated disease. Regardless of clinical severity, LCH lesions share the common histology of CD1a(+)/CD207(+) dendritic cells with characteristic morphology among an inflammatory infiltrate. Despite historical uncertainty defining LCH as inflammatory vs neoplastic and incomplete understanding of mechanisms of pathogenesis, clinical outcomes have improved markedly over the past decades through cooperative randomized clinical trials based on empiric therapeutic strategies. Significant advances include recognition of high- and low-risk clinical groups defined by hematopoietic and/or hepatic involvement, and of the importance of optimal intensity and of duration of chemotherapy. Nevertheless, mortality of high-risk patients, disease recurrence, lack of robustly tested salvage strategies, and significant disease morbidity of both high- and low-risk patients remain challenges. Recent discovery of recurrent somatic mutations in mitogen-activated protein kinase pathway genes at critical stages of myeloid hematopoietic differentiation in LCH patients supports redefinition of the disease as a myeloproliferative disorder and provides opportunities to develop novel approaches to diagnosis and therapy.
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18
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Abstract
Although there have been dramatic improvements in the treatment of children with non-hodgkin lymphoma, hodgkin lymphoma and histiocytic disorders over the past 3 decades, many still relapse or are refractory to primary therapy. In addition, late effects such as 2nd malignancies, cardiomyopathy and infertility remain a major concern. Thus, this review focuses on the current state of the science and, in particular, novel treatment strategies that are aimed at improving outcomes for all pediatric patients with lymphoma and histiocytic disorders while reducing treatment related morbidity.
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Affiliation(s)
- Carl E Allen
- Department of Pediatrics, Texas Children's Cancer Center, Baylor College of Medicine, 1102 Bates St, Houston, TX 77030, USA
| | - Kara M Kelly
- Herbert Irving Child and Adolescent Oncology Center, Morgan Stanley Children's Hospital, New York-Presbyterian, Columbia University Medical Center, 161 Fort Washington Ave, New York, NY 10032, USA
| | - Catherine M Bollard
- Program for Cell Enhancement and Technologies for Immunotherapy, BMT Division, Department of Pediatrics, Children's National Health System, The George Washington University, 111 Michigan Avenue, Northwest, Washington, DC 20010, USA.
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19
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Berres ML, Merad M, Allen CE. Progress in understanding the pathogenesis of Langerhans cell histiocytosis: back to Histiocytosis X? Br J Haematol 2014; 169:3-13. [PMID: 25430560 DOI: 10.1111/bjh.13247] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Langerhans cell histiocytosis (LCH), the most common histiocytic disorder, is characterized by the accumulation of CD1A(+) /CD207(+) mononuclear phagocytes within granulomatous lesions that can affect nearly all organ systems. Historically, LCH has been presumed to arise from transformed or pathologically activated epidermal dendritic cells called Langerhans cells. However, new evidence supports a model in which LCH occurs as a consequence of a misguided differentiation programme of myeloid dendritic cell precursors. Genetic, molecular and functional data implicate activation of the ERK signalling pathway at critical stages in myeloid differentiation as an essential and universal driver of LCH pathology. Based on these findings, we propose that LCH should be re-defined as an inflammatory myeloid neoplasia. Increased understanding of LCH pathogenesis will provide opportunities to optimize and personalize therapy through improved risk-stratification, targeted therapy and assessment of therapy response based on specific molecular features and origin of the pathological myeloid cells.
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Affiliation(s)
- Marie-Luise Berres
- Department of Oncological Sciences, Mount Sinai School of Medicine, New York, NY, USA; Tisch Cancer Institute, Mount Sinai School of Medicine, New York, NY, USA; Immunology Institute, Mount Sinai School of Medicine, New York, NY, USA; Department of Internal Medicine III, University Hospital, RWTH Aachen, Aachen, Germany
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20
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Mao Y, Chen H, Liang H, Meric-Bernstam F, Mills GB, Chen K. CanDrA: cancer-specific driver missense mutation annotation with optimized features. PLoS One 2013; 8:e77945. [PMID: 24205039 PMCID: PMC3813554 DOI: 10.1371/journal.pone.0077945] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 09/05/2013] [Indexed: 01/24/2023] Open
Abstract
Driver mutations are somatic mutations that provide growth advantage to tumor cells, while passenger mutations are those not functionally related to oncogenesis. Distinguishing drivers from passengers is challenging because drivers occur much less frequently than passengers, they tend to have low prevalence, their functions are multifactorial and not intuitively obvious. Missense mutations are excellent candidates as drivers, as they occur more frequently and are potentially easier to identify than other types of mutations. Although several methods have been developed for predicting the functional impact of missense mutations, only a few have been specifically designed for identifying driver mutations. As more mutations are being discovered, more accurate predictive models can be developed using machine learning approaches that systematically characterize the commonality and peculiarity of missense mutations under the background of specific cancer types. Here, we present a cancer driver annotation (CanDrA) tool that predicts missense driver mutations based on a set of 95 structural and evolutionary features computed by over 10 functional prediction algorithms such as CHASM, SIFT, and MutationAssessor. Through feature optimization and supervised training, CanDrA outperforms existing tools in analyzing the glioblastoma multiforme and ovarian carcinoma data sets in The Cancer Genome Atlas and the Cancer Cell Line Encyclopedia project.
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Affiliation(s)
- Yong Mao
- Department of Bioinformatics and Computational Biology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Han Chen
- Department of Bioinformatics and Computational Biology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Funda Meric-Bernstam
- Department of Surgical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Gordon B. Mills
- Department of Systems Biology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail:
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21
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Kline CLB, El-Deiry WS. Personalizing colon cancer therapeutics: targeting old and new mechanisms of action. Pharmaceuticals (Basel) 2013; 6:988-1038. [PMID: 24276379 PMCID: PMC3817731 DOI: 10.3390/ph6080988] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 07/30/2013] [Accepted: 08/16/2013] [Indexed: 12/17/2022] Open
Abstract
The use of pharmaceuticals for colon cancer treatment has been increasingly personalized, in part due to the development of new molecular tools. In this review, we discuss the old and new colon cancer chemotherapeutics, and the parameters that have been shown to be predictive of efficacy and safety of these chemotherapeutics. In addition, we discuss how alternate pharmaceuticals have been developed in light of a potential lack of response or resistance to a particular chemotherapeutic.
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Affiliation(s)
- Christina Leah B Kline
- Hematology/Oncology Division, Penn State Hershey Medical Center, Hershey, PA 17033, USA.
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22
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Su F, Correa BRS, Luo J, Vencio RZN, Pascal LE, Wang Z. Gene Expression Profiling Reveals Regulation of ERK Phosphorylation by Androgen-Induced Tumor Suppressor U19/EAF2 in the Mouse Prostate. CANCER MICROENVIRONMENT 2013; 6:247-61. [PMID: 23440596 DOI: 10.1007/s12307-013-0132-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 02/12/2013] [Indexed: 01/02/2023]
Abstract
U19/EAF2 is regulated by androgens in the prostate and capable of regulating transcriptional elongation of RNA Pol II via interaction with the ELL family proteins. Inactivation of U19/EAF2 induces tumorigenesis in multiple organs; however the mechanism of U19/EAF2 tumor suppression remains unclear. To elucidate potential mechanisms of U19/EAF2 action, we performed cDNA microarray analysis and identified 164 mRNA transcripts regulated by U19/EAF2 in the mouse ventral prostate. Bioinformatics analysis indicated that U19/EAF2 knockout activates the RAS-BRAF-ERK signaling pathway, which is known to play important roles in carcinogenesis. qPCR verified increased expression of BRAF mRNA, and immunostaining and Western blot analysis demonstrated increased expression of p-ERK at the protein level suggested U19/EAF2 knockout activates this important pathway. These findings indicate that loss of EAF2 up-regulates transcription of RAS cascade genes including Grb2, PI3K, and BRAF, leading to elevated p-ERK levels, which may represent a major functional role of U19/EAF2 in the prostate. Furthermore, these observations suggest that U19/EAF2 is a key player in crosstalk between androgen receptor and the RAS-BRAF-ERK signaling pathway.
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Affiliation(s)
- Fei Su
- Department of Urology, University of Pittsburgh, Pittsburgh, PA, 15232, USA
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23
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Huber F, Lang HP, Backmann N, Rimoldi D, Gerber C. Direct detection of a BRAF mutation in total RNA from melanoma cells using cantilever arrays. NATURE NANOTECHNOLOGY 2013; 8:125-129. [PMID: 23377457 DOI: 10.1038/nnano.2012.263] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 12/18/2012] [Indexed: 05/27/2023]
Abstract
Malignant melanoma, the deadliest form of skin cancer, is characterized by a predominant mutation in the BRAF gene. Drugs that target tumours carrying this mutation have recently entered the clinic. Accordingly, patients are routinely screened for mutations in this gene to determine whether they can benefit from this type of treatment. The current gold standard for mutation screening uses real-time polymerase chain reaction and sequencing methods. Here we show that an assay based on microcantilever arrays can detect the mutation nanomechanically without amplification in total RNA samples isolated from melanoma cells. The assay is based on a BRAF-specific oligonucleotide probe. We detected mutant BRAF at a concentration of 500 pM in a 50-fold excess of the wild-type sequence. The method was able to distinguish melanoma cells carrying the mutation from wild-type cells using as little as 20 ng µl(-1) of RNA material, without prior PCR amplification and use of labels.
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Affiliation(s)
- F Huber
- Swiss Nano Institute, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland.
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