1
|
Goldstein Y, Cohen OT, Wald O, Bavli D, Kaplan T, Benny O. Particle uptake in cancer cells can predict malignancy and drug resistance using machine learning. SCIENCE ADVANCES 2024; 10:eadj4370. [PMID: 38809990 DOI: 10.1126/sciadv.adj4370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 04/23/2024] [Indexed: 05/31/2024]
Abstract
Tumor heterogeneity is a primary factor that contributes to treatment failure. Predictive tools, capable of classifying cancer cells based on their functions, may substantially enhance therapy and extend patient life span. The connection between cell biomechanics and cancer cell functions is used here to classify cells through mechanical measurements, via particle uptake. Machine learning (ML) was used to classify cells based on single-cell patterns of uptake of particles with diverse sizes. Three pairs of human cancer cell subpopulations, varied in their level of drug resistance or malignancy, were studied. Cells were allowed to interact with fluorescently labeled polystyrene particles ranging in size from 0.04 to 3.36 μm and analyzed for their uptake patterns using flow cytometry. ML algorithms accurately classified cancer cell subtypes with accuracy rates exceeding 95%. The uptake data were especially advantageous for morphologically similar cell subpopulations. Moreover, the uptake data were found to serve as a form of "normalization" that could reduce variation in repeated experiments.
Collapse
Affiliation(s)
- Yoel Goldstein
- Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Ora T Cohen
- Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Ori Wald
- Department of Cardiothoracic Surgery, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Danny Bavli
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| | - Ofra Benny
- Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112001, Israel
| |
Collapse
|
2
|
He P, Du L, Dai Q, Li G, Yu B, Chang L. Design, synthesis and biological evaluation of structurally new 4-indolyl quinazoline derivatives as highly potent, selective and orally bioavailable EGFR inhibitors. Bioorg Chem 2024; 142:106970. [PMID: 37984101 DOI: 10.1016/j.bioorg.2023.106970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
Targeting the epidermal growth factor receptor (EGFR) has been recognized as an effective strategy for treating non-small-cell lung cancer (NSCLC). Although several representative EGFR inhibitors have been approved for clinical use, it is highly desirable to develop highly potent and selective EGFR inhibitors with novel scaffolds because of the occurrence of acquired resistance after treatment. Here we first demonstrate that the 4-indolyl quinazoline derivatives could potently inhibit EGFR in vitro and in vivo, of which YS-67 effectively and selectively inhibits EGFR[WT] (IC50 = 5.2 nM), EGFR[d746-750] (IC50 = 9.6 nM) and EGFR[L858R] (IC50 = 1.9 nM). The TREEspot™ kinase interaction map further reveals the binding selectivity toward 468 kinases. YS-67 not only potently suppresses p-EGFR and p-AKT, but also effectively inhibits proliferation of A549 (IC50 = 4.1 μM), PC-9 (IC50 = 0.5 μM) and A431 cells (IC50 = 2.1 μM). YS-67 treatment also causes colony formation inhibition, arrests cell cycle progression at G0/G1 phases and induces apoptosis. More importantly, YS-67 is well tolerated in A431 xenograft model after oral administration, showing effective tumor growth suppression and low toxicity. Collectively, YS-67 represents an underexplored scaffold for developing new EGFR inhibitors.
Collapse
Affiliation(s)
- Pengxing He
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Linna Du
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Qingqing Dai
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Guobo Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Bin Yu
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China; Pingyuan Laboratory, State Key Laboratory of Antiviral Drugs, Henan Normal University, Xinxiang, Henan 453007 China.
| | - Linlin Chang
- Department of Pharmacy, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Henan Provincial Key Laboratory of Anticancer Drug Research, Henan Cancer Hospital, Zhengzhou 450008, China.
| |
Collapse
|
3
|
Gurav M, Epari S, Gogte P, Pai T, Deshpande G, Karnik N, Shetty O, Desai S. Targeted molecular profiling of solid tumours-Indian tertiary cancer centre experience. J Cancer Res Clin Oncol 2023; 149:7413-7425. [PMID: 36935431 DOI: 10.1007/s00432-023-04693-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/12/2023] [Indexed: 03/21/2023]
Abstract
PURPOSE Molecular Profiling of solid tumours is extensively used for prognostic, theranostic, and risk prediction. Next generation sequencing (NGS) has emerged as powerful method for molecular profiling. The present study was performed to identify molecular alterations present in solid tumours in Indian tertiary cancer centre. METHODS Study included 1140 formalin Fixed paraffin embedded samples. NGS was performed using two targeted gene panels viz. Ampliseq Focus panel and Sophia Solid Tumor Plus Solution. Data was analyzed using Illumina's Local Run Manager and SOPHiA DDM software. Variant interpretation and annotations were done as per AMP/ACMG guidelines. RESULTS Total 896 cases were subjected to NGS after excluding cases with suboptimal nucleic acid quality/quantity. DNA alterations were detected in 64.9% and RNA fusions in 6.9% cases. Among detected variants, 86.7% were clinically relevant aberrations. Mutation frequency among different solid tumours was 70.8%, 67.4%, 64.4% in non-small cell lung (NSCLC), lung squamous cell carcinomas and head neck tumours respectively. EGFR, KRAS, BRAF, ALK and ROS1were commonly altered in NSCLC. Gastrointestinal tumours showed mutations in 63.6% with predominant alterations in pancreatic (88.2%), GIST (87.5%), colorectal (78.7%), cholangiocarcinoma (52.9%), neuroendocrine (45.5%), gall bladder (36.7%) and gastric adenocarcinomas (16.7%). The key genes affected were KRAS, NRAS, BRAF and PIK3CA. NGS evaluation identified co-occurring alterations in 37.7% cases otherwise missed by conventional assays. Resistance mutations were detected in progressive lung tumours (39.5%) against EGFR TKIs and ALK/ROS inhibitors. CONCLUSION This is the largest Indian study on molecular profiling of solid tumours providing extensive information about mutational signatures using NGS.
Collapse
Affiliation(s)
- Mamta Gurav
- Molecular Pathology laboratory, Department of Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Sridhar Epari
- Department of Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Prachi Gogte
- Molecular Pathology laboratory, Department of Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Trupti Pai
- Department of Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Gauri Deshpande
- Department of Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Nupur Karnik
- Department of Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Omshree Shetty
- Molecular Pathology laboratory, Department of Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India.
| | - Sangeeta Desai
- Department of Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| |
Collapse
|
4
|
Ghosn M, Elsakka AS, Petre EN, Cheleuitte-Nieves C, Tammela T, Monette S, Ziv E, Schachtschneider KM, Srimathveeravalli G, Yarmohammadi H, Edward Boas F, Solomon SB. Induction and preliminary characterization of neoplastic pulmonary nodules in a transgenic pig model. Lung Cancer 2023; 178:157-165. [PMID: 36868176 PMCID: PMC10538441 DOI: 10.1016/j.lungcan.2023.02.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 01/09/2023] [Accepted: 02/16/2023] [Indexed: 02/25/2023]
Abstract
OBJECTIVES Lung cancer models in large animals are lacking. Oncopigs are transgenic pigs that carry both KRASG12D and TP53R167H Cre-inducible mutations. This study aimed to develop and histologically characterize a swine model of lung cancer that could serve for preclinical studies evaluating locoregional therapies. MATERIALS AND METHODS In two Oncopigs, an adenoviral vector encoding the Cre-recombinase gene (AdCre) was injected endovascularly through the pulmonary arteries or inferior vena cava. In two other Oncopigs, a lung biopsy was performed and incubated with AdCre, before reinjecting the mixture into the lungs percutaneously. Animals were clinically and biologically (complete blood count, liver enzymes and lipasemia) monitored. Obtained tumors were characterized on computed tomography (CT) and on pathology and immunohistochemistry (IHC). RESULTS Neoplastic lung nodules developed following 1 (1/10, 10%) endovascular inoculation, and 2 (2/6, 33%) percutaneous inoculations. All lung tumors were visible at the 1-week CT, and appeared as well-circumscribed solid nodules, with a median longest diameter of 14 mm (range: 5-27 mm). Only one complication occurred: an extravasation of the mixture into the thoracic wall during a percutaneous injection that resulted in a thoracic wall tumor. Pigs remained clinically healthy during the entire follow-up (14-21 days). On histology, tumors consisted of inflammatory undifferentiated neoplasms composed of atypical spindle and epithelioid cells and/or a fibrovascular stroma and abundant mixed leukocytic infiltrate. On IHC, atypical cells diffusely displayed expression of vimentin and some showed expression of CK WSS and CK 8/18. The tumor microenvironment contained abundant IBA1 + macrophages and giant cells, CD3 + T cells, and CD31 + blood vessels. CONCLUSION Tumors induced in the lungs of Oncopigs are fast growing poorly differentiated neoplasms associated with a marked inflammatory reaction that can be easily and safely induced at site specific locations. This large animal model might be suitable for interventional and surgical therapies of lung cancer.
Collapse
Affiliation(s)
- Mario Ghosn
- Department of Interventional Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Ahmed S Elsakka
- Department of Interventional Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Elena N Petre
- Department of Interventional Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Christopher Cheleuitte-Nieves
- Center of Comparative Medicine and Pathology, Memorial Sloan Kettering Cancer Center and Weill Cornell Medicine, New York, NY, USA
| | - Tuomas Tammela
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sebastien Monette
- Laboratory of Comparative Pathology, Memorial Sloan Kettering Cancer Center, The Rockefeller University, Weill Cornell Medicine, New York, NY, USA
| | - Etay Ziv
- Department of Interventional Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Kyle M Schachtschneider
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA; Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA; National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Govind Srimathveeravalli
- Department of Mechanical Engineering, Institute for Applied Life Sciences, University of Massachusetts Amherst, Life Sciences Laboratories, 240 Thatcher Road Amherst, MA, USA
| | - Hooman Yarmohammadi
- Department of Interventional Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - F Edward Boas
- Department of Radiology, City of Hope Cancer Center, 1500 East Duarte Rd., Duarte, CA, USA
| | - Stephen B Solomon
- Department of Interventional Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA.
| |
Collapse
|
5
|
Freire Boullosa L, Van Loenhout J, Flieswasser T, Hermans C, Merlin C, Lau HW, Marcq E, Verschuuren M, De Vos WH, Lardon F, Smits ELJ, Deben C. Auranofin Synergizes with the PARP Inhibitor Olaparib to Induce ROS-Mediated Cell Death in Mutant p53 Cancers. Antioxidants (Basel) 2023; 12:antiox12030667. [PMID: 36978917 PMCID: PMC10045521 DOI: 10.3390/antiox12030667] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/23/2023] [Accepted: 03/03/2023] [Indexed: 03/11/2023] Open
Abstract
Auranofin (AF) is a potent, off-patent thioredoxin reductase (TrxR) inhibitor that efficiently targets cancer via reactive oxygen species (ROS)- and DNA damage-mediated cell death. The goal of this study is to enhance the efficacy of AF as a cancer treatment by combining it with the poly(ADP-ribose) polymerase-1 (PARP) inhibitor olaparib (referred to as ‘aurola’). Firstly, we investigated whether mutant p53 can sensitize non-small cell lung cancer (NSCLC) and pancreatic ductal adenocarcinoma (PDAC) cancer cells to AF and olaparib treatment in p53 knock-in and knock-out models with varying p53 protein expression levels. Secondly, we determined the therapeutic range for synergistic cytotoxicity between AF and olaparib and elucidated the underlying molecular cell death mechanisms. Lastly, we evaluated the effectiveness of the combination strategy in a murine 344SQ 3D spheroid and syngeneic in vivo lung cancer model. We demonstrated that high concentrations of AF and olaparib synergistically induced cytotoxicity in NSCLC and PDAC cell lines with low levels of mutant p53 protein that were initially more resistant to AF. The aurola combination also led to the highest accumulation of ROS, which resulted in ROS-dependent cytotoxicity of mutant p53 NSCLC cells through distinct types of cell death, including caspase-3/7-dependent apoptosis, inhibited by Z-VAD-FMK, and lipid peroxidation-dependent ferroptosis, inhibited by ferrostatin-1 and alpha-tocopherol. High concentrations of both compounds were also needed to obtain a synergistic cytotoxic effect in 3D spheroids of the murine lung adenocarcinoma cell line 344SQ, which was interestingly absent in 2D. This cell line was used in a syngeneic mouse model in which the oral administration of aurola significantly delayed the growth of mutant p53 344SQ tumors in 129S2/SvPasCrl mice, while either agent alone had no effect. In addition, RNA sequencing results revealed that AF- and aurola-treated 344SQ tumors were negatively enriched for immune-related gene sets, which is in accordance with AF’s anti-inflammatory function as an anti-rheumatic drug. Only 344SQ tumors treated with aurola showed the downregulation of genes related to the cell cycle, potentially explaining the growth inhibitory effect of aurola since no apoptosis-related gene sets were enriched. Overall, this novel combination strategy of oxidative stress induction (AF) with PARP inhibition (olaparib) could be a promising treatment for mutant p53 cancers, although high concentrations of both compounds need to be reached to obtain a substantial cytotoxic effect.
Collapse
Affiliation(s)
- Laurie Freire Boullosa
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, 2610 Wilrijk, Belgium
| | - Jinthe Van Loenhout
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, 2610 Wilrijk, Belgium
| | - Tal Flieswasser
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, 2610 Wilrijk, Belgium
| | - Christophe Hermans
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, 2610 Wilrijk, Belgium
| | - Céline Merlin
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, 2610 Wilrijk, Belgium
| | - Ho Wa Lau
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, 2610 Wilrijk, Belgium
| | - Elly Marcq
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, 2610 Wilrijk, Belgium
| | - Marlies Verschuuren
- Laboratory of Cell Biology and Histology, Antwerp Center for Advanced Microscopy, Department of Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium
- µNEURO Research Centre of Excellence, University of Antwerp, 2610 Wilrijk, Belgium
| | - Winnok H. De Vos
- Laboratory of Cell Biology and Histology, Antwerp Center for Advanced Microscopy, Department of Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium
- µNEURO Research Centre of Excellence, University of Antwerp, 2610 Wilrijk, Belgium
| | - Filip Lardon
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, 2610 Wilrijk, Belgium
| | - Evelien L. J. Smits
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, 2610 Wilrijk, Belgium
| | - Christophe Deben
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, 2610 Wilrijk, Belgium
- Correspondence: ; Tel.: +32-3-265-25-76
| |
Collapse
|
6
|
Nishio M, Paz-Ares L, Reck M, Nakagawa K, Garon EB, Popat S, Ceccarelli M, Graham HT, Visseren-Grul C, Novello S. RELAY, Ramucirumab plus Erlotinib (RAM+ERL) in Untreated Metastatic EGFR-Mutant NSCLC (EGFR+ NSCLC): Association between TP53 Status and Clinical Outcome. Clin Lung Cancer 2023:S1525-7304(23)00046-3. [PMID: 37076395 DOI: 10.1016/j.cllc.2023.02.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 04/03/2023]
Abstract
BACKGROUND Ramucirumab plus erlotinib (RAM+ERL) demonstrated superior progression-free survival (PFS) in RELAY, a randomised Phase III trial in patients with untreated, metastatic, EGFR-mutated, non-small-cell lung cancer (EGFR+ NSCLC). Here, we present the relationship between TP53 status and outcomes in RELAY. MATERIALS AND METHODS Patients received oral ERL plus intravenous RAM (10 mg/kg IV) or placebo (PBO+ERL) every 2 weeks. Plasma was assessed by Guardant 360 next-generation sequencing and patients with any gene alteration detected at baseline were included in this exploratory analysis. Endpoints included PFS, overall response rate (ORR), disease control rate (DCR), DoR, overall survival (OS), safety, and biomarker analysis. The association between TP53 status and outcomes was evaluated. RESULTS Mutated TP53 was detected in 165 (42.7%; 74 RAM+ERL, 91 PBO+ERL) patients, wild-type TP53 in 221 (57.3%; 118 RAM+ERL, 103 PBO+ERL) patients. Patient and disease characteristics and concurrent gene alterations were comparable between those with mutant and wildtype TP53. Independent of treatment, TP53 mutations, most notably on exon 8, were associated with worse clinical outcomes. In all patients, RAM+ERL improved PFS. While ORR and DCR were comparable across all patients, DoR was superior with RAM+ERL. There were no clinically meaningful differences in the safety profiles between those with baseline TP53 mutation and wild-type. CONCLUSION This analysis indicates that while TP53 mutations are a negative prognostic marker in EGFR+ NSCLC, the addition of a VEGF inhibitor improves outcomes in those with mutant TP53. RAM+ERL is an efficacious first-line treatment option for patients with EGFR+ NSCLC, independent of TP53 status.
Collapse
Affiliation(s)
- Makoto Nishio
- Department of Thoracic Medical Oncology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan.
| | - Luis Paz-Ares
- Medical Oncology Department, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Martin Reck
- Department of Thoracic Oncology, LungenClinic, Airway Research Center North, German Center for Lung Research, Grosshansdorf, Germany
| | - Kazuhiko Nakagawa
- Department of Medical Oncology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Edward B Garon
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Sanjay Popat
- Lung Unit, Royal Marsden NHS Trust, London, United Kingdom
| | - Matteo Ceccarelli
- Global Clinical Development, Eli Lilly and Company, Sesto Fiorentino, Florence, Italy
| | | | - Carla Visseren-Grul
- Global Clinical Development, Eli Lilly Netherlands, Utrecht, The Netherlands
| | - Silvia Novello
- Department of Oncology, University of Turin, San Luigi Hospital, Turin, Italy
| |
Collapse
|
7
|
Parma B, Wurdak H, Ceppi P. Harnessing mitochondrial metabolism and drug resistance in non-small cell lung cancer and beyond by blocking heat-shock proteins. Drug Resist Updat 2022; 65:100888. [DOI: 10.1016/j.drup.2022.100888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/10/2022] [Accepted: 10/25/2022] [Indexed: 11/30/2022]
|
8
|
Aljamal AA, Elajami MK, Mansour EH, Bahmad HF, Medina AM, Cusnir M. Novel ATM Gene c.5644 C > T (p.Arg1882*) Variant Detected in a Patient with Pancreatic Adenocarcinoma and Two Primary Non-Small Cell Lung Adenocarcinomas: A Case Report. Diseases 2022; 10:diseases10040115. [PMID: 36547201 PMCID: PMC9778013 DOI: 10.3390/diseases10040115] [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: 10/16/2022] [Revised: 11/04/2022] [Accepted: 11/29/2022] [Indexed: 12/05/2022] Open
Abstract
Ataxia-telangiectasia is an autosomal recessive disorder that usually manifests in childhood due to mutations in the Ataxia-Telangiectasia Mutated (ATM) gene. It is believed that there is an association between this gene mutation/polymorphism and cancer risk, including breast, lung, and pancreatic cancers. We report a rare case of a 69-year-old woman who developed three different primary cancers, including non-small cell lung cancer (NSCLC) in both lungs and pancreatic adenocarcinoma, and was later found to have a rarely reported variant mutation in the ATM gene, namely Exon 39, c.5644 C > T. We hypothesize that the ATM gene, c.5644 C > T mutation could be a plausible contributor in the pathogenesis of these three cancers. This hypothesis has yet to be validated by larger studies that focus on a mechanistic approach involving DNA repair genes such as the ATM. More importantly, this paves the way to developing new patient-specific targeted therapies and inaugurating precision medicine as a cornerstone in cancer therapeutics.
Collapse
Affiliation(s)
- Abed A. Aljamal
- Mount Sinai Medical Center, Department of Internal Medicine, Miami Beach, FL 33140, USA
- Department of Medicine, Division of Hematology Oncology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Mohamad K. Elajami
- Mount Sinai Medical Center, Department of Internal Medicine, Miami Beach, FL 33140, USA
| | - Ephraim H. Mansour
- Mount Sinai Medical Center, Department of Internal Medicine, Miami Beach, FL 33140, USA
| | - Hisham F. Bahmad
- The Arkadi M. Rywlin M.D. Department of Pathology and Laboratory Medicine, Mount Sinai Medical Center, Miami Beach, FL 33140, USA
- Correspondence: or ; Tel.: +1-305-674-2277
| | - Ana Maria Medina
- The Arkadi M. Rywlin M.D. Department of Pathology and Laboratory Medicine, Mount Sinai Medical Center, Miami Beach, FL 33140, USA
- Department of Translational Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Mike Cusnir
- Mount Sinai Medical Center, Department of Internal Medicine, Division of Hematology and Oncology, Miami Beach, FL 33140, USA
| |
Collapse
|
9
|
Maraqa B, Al-Ashhab M, Sughayer MA. Anaplastic lymphoma kinase rearrangements in patients with non-small cell lung cancer in Jordan. J Int Med Res 2022; 50:3000605221104181. [PMID: 35689392 PMCID: PMC9189535 DOI: 10.1177/03000605221104181] [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] [Indexed: 11/23/2022] Open
Abstract
Objective Anaplastic lymphoma kinase (ALK) rearrangement is an important oncogenic driver in some non-small cell lung cancers (NSCLC). Treatment with ALK tyrosine kinase inhibitors improves survival. The availability of diagnostic immunohistochemistry (IHC) has led to a paradigm shift in ALK testing. This study examined the prevalence of ALK rearrangement in Jordanian patients with NSCLC and compared the results of IHC and fluorescence in situ hybridization (FISH) for detecting ALK rearrangement. Methods This retrospective study on 449 patients with NSCLC treated at the King Hussein Cancer Center in Jordan tested biopsy samples for ALK rearrangement using FISH and/or IHC (D5F3) between 2018 and 2020. Results Eighteen patients (4%) had ALK-positive NSCLC. The calculated sensitivity and specificity of ALK immunostaining compared with FISH were 87.5% and 96%, respectively. ALK-positive patients were significantly younger than their ALK-negative counterparts, and women were three times more likely to carry ALK rearrangement than men. ALK rearrangement was significantly associated with smoking history, with most ALK-positive patients being non-smokers, former smokers, or light smokers. Conclusions IHC is a reasonable alternative to FISH for ALK testing with advantages in terms of robustness, turnaround times, and cost-effectiveness.
Collapse
Affiliation(s)
- Bayan Maraqa
- Department of Pathology and Laboratory Medicine, King Hussein Cancer Center, Amman, Jordan
| | - Maxim Al-Ashhab
- Department of Pathology and Laboratory Medicine, King Hussein Cancer Center, Amman, Jordan
| | - Maher A Sughayer
- Department of Pathology and Laboratory Medicine, King Hussein Cancer Center, Amman, Jordan
| |
Collapse
|
10
|
Fahrmann JF, Tanaka I, Irajizad E, Mao X, Dennison JB, Murage E, Casabar J, Mayo J, Peng Q, Celiktas M, Vykoukal JV, Park S, Taguchi A, Delgado O, Tripathi SC, Katayama H, Soto LMS, Rodriguez-Canales J, Behrens C, Wistuba I, Hanash S, Ostrin EJ. Mutational Activation of the NRF2 Pathway Upregulates Kynureninase Resulting in Tumor Immunosuppression and Poor Outcome in Lung Adenocarcinoma. Cancers (Basel) 2022; 14:2543. [PMID: 35626147 PMCID: PMC9139317 DOI: 10.3390/cancers14102543] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/13/2022] [Accepted: 05/17/2022] [Indexed: 11/17/2022] Open
Abstract
Activation of the NRF2 pathway through gain-of-function mutations or loss-of-function of its suppressor KEAP1 is a frequent finding in lung cancer. NRF2 activation has been reported to alter the tumor microenvironment. Here, we demonstrated that NRF2 alters tryptophan metabolism through the kynurenine pathway that is associated with a tumor-promoting, immune suppressed microenvironment. Specifically, proteomic profiles of 47 lung adenocarcinoma (LUAD) cell lines (11 KEAP1 mutant and 36 KEAP1 wild-type) revealed the tryptophan-kynurenine enzyme kynureninase (KYNU) as a top overexpressed protein associated with activated NRF2. The siRNA-mediated knockdown of NFE2L2, the gene encoding for NRF2, or activation of the NRF2 pathway through siRNA-mediated knockdown of KEAP1 or via chemical induction with the NRF2-activator CDDO-Me confirmed that NRF2 is a regulator of KYNU expression in LUAD. Metabolomic analyses confirmed KYNU to be enzymatically functional. Analysis of multiple independent gene expression datasets of LUAD, as well as a LUAD tumor microarray demonstrated that elevated KYNU was associated with immunosuppression, including potent induction of T-regulatory cells, increased levels of PD1 and PD-L1, and resulted in poorer survival. Our findings indicate a novel mechanism of NRF2 tumoral immunosuppression through upregulation of KYNU.
Collapse
Affiliation(s)
- Johannes F. Fahrmann
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (J.F.F.); (X.M.); (J.B.D.); (E.M.); (J.C.); (M.C.); (J.V.V.); (S.P.); (O.D.); (H.K.); (S.H.)
| | - Ichidai Tanaka
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya 464-8601, Japan;
| | - Ehsan Irajizad
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA;
| | - Xiangying Mao
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (J.F.F.); (X.M.); (J.B.D.); (E.M.); (J.C.); (M.C.); (J.V.V.); (S.P.); (O.D.); (H.K.); (S.H.)
| | - Jennifer B. Dennison
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (J.F.F.); (X.M.); (J.B.D.); (E.M.); (J.C.); (M.C.); (J.V.V.); (S.P.); (O.D.); (H.K.); (S.H.)
| | - Eunice Murage
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (J.F.F.); (X.M.); (J.B.D.); (E.M.); (J.C.); (M.C.); (J.V.V.); (S.P.); (O.D.); (H.K.); (S.H.)
| | - Julian Casabar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (J.F.F.); (X.M.); (J.B.D.); (E.M.); (J.C.); (M.C.); (J.V.V.); (S.P.); (O.D.); (H.K.); (S.H.)
| | - Jeffrey Mayo
- Department of General Internal Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (J.M.); (Q.P.)
| | - Qian Peng
- Department of General Internal Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (J.M.); (Q.P.)
| | - Muge Celiktas
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (J.F.F.); (X.M.); (J.B.D.); (E.M.); (J.C.); (M.C.); (J.V.V.); (S.P.); (O.D.); (H.K.); (S.H.)
| | - Jody V. Vykoukal
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (J.F.F.); (X.M.); (J.B.D.); (E.M.); (J.C.); (M.C.); (J.V.V.); (S.P.); (O.D.); (H.K.); (S.H.)
| | - Soyoung Park
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (J.F.F.); (X.M.); (J.B.D.); (E.M.); (J.C.); (M.C.); (J.V.V.); (S.P.); (O.D.); (H.K.); (S.H.)
| | - Ayumu Taguchi
- Division of Molecular Diagnostics, Aichi Cancer Center, Kanokoden, Chikusa-ku, Nagoya 464-8681, Japan;
| | - Oliver Delgado
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (J.F.F.); (X.M.); (J.B.D.); (E.M.); (J.C.); (M.C.); (J.V.V.); (S.P.); (O.D.); (H.K.); (S.H.)
| | | | - Hiroyuki Katayama
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (J.F.F.); (X.M.); (J.B.D.); (E.M.); (J.C.); (M.C.); (J.V.V.); (S.P.); (O.D.); (H.K.); (S.H.)
| | - Luisa Maren Solis Soto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (L.M.S.S.); (J.R.-C.); (C.B.); (I.W.)
| | - Jaime Rodriguez-Canales
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (L.M.S.S.); (J.R.-C.); (C.B.); (I.W.)
| | - Carmen Behrens
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (L.M.S.S.); (J.R.-C.); (C.B.); (I.W.)
| | - Ignacio Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (L.M.S.S.); (J.R.-C.); (C.B.); (I.W.)
| | - Samir Hanash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (J.F.F.); (X.M.); (J.B.D.); (E.M.); (J.C.); (M.C.); (J.V.V.); (S.P.); (O.D.); (H.K.); (S.H.)
| | - Edwin J. Ostrin
- Department of General Internal Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (J.M.); (Q.P.)
| |
Collapse
|
11
|
Bruns IB, Beltman JB. Quantifying the contribution of transcription factor activity, mutations and microRNAs to CD274 expression in cancer patients. Sci Rep 2022; 12:4374. [PMID: 35289334 PMCID: PMC8921511 DOI: 10.1038/s41598-022-08356-0] [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: 09/20/2021] [Accepted: 03/03/2022] [Indexed: 12/15/2022] Open
Abstract
Immune checkpoint inhibitors targeting the programmed cell death protein 1 (PD-1)/programmed cell death protein ligand 1 (PD-L1) axis have been remarkably successful in inducing tumor remissions in several human cancers, yet a substantial number of patients do not respond to treatment. Because this may be partially due to the mechanisms giving rise to high PD-L1 expression within a patient, it is highly relevant to fully understand these mechanisms. In this study, we conduct a bioinformatic analysis to quantify the relative importance of transcription factor (TF) activity, microRNAs (miRNAs) and mutations in determining PD-L1 (CD274) expression at mRNA level based on data from the Cancer Genome Atlas. To predict individual CD274 levels based on TF activity, we developed multiple linear regression models by taking the expression of target genes of the TFs known to directly target PD-L1 as independent variables. This analysis showed that IRF1, STAT1, NFKB and BRD4 are the most important regulators of CD274 expression, explaining its mRNA levels in 90–98% of the patients. Because the remaining patients had high CD274 levels independent of these TFs, we next investigated whether mutations associated with increased CD274 mRNA levels, and low levels of miRNAs associated with negative regulation of CD274 expression could cause high CD274 levels in these patients. We found that mutations or miRNAs offered an explanation for high CD274 levels in 81–100% of the underpredicted patients. Thus, CD274 expression is largely explained by TF activity, and the remaining unexplained cases can largely be explained by mutations or low miRNA abundance.
Collapse
Affiliation(s)
- Imke B Bruns
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Joost B Beltman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands.
| |
Collapse
|
12
|
Dominguez-Martinez I, Joaquin-Ovalle F, Ferrer-Acosta Y, Griebenow KH. Folate-Decorated Cross-Linked Cytochrome c Nanoparticles for Active Targeting of Non-Small Cell Lung Carcinoma (NSCLC). Pharmaceutics 2022. [DOI: https://doi.org/10.3390/pharmaceutics14030490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The folate receptor alpha (FR), which is overexpressed in solid tumors including NSCLC, can be utilized for active tumor targeting to afford more effective cancer therapies. In this context, cytochrome c (Cyt c) has drawn attention to cancer research because it is non-toxic, yet, when delivered to the cytoplasm of cancer cells, can kill them by inducing apoptosis. Cyt c nanoparticles (NPs, 169 ± 9 nm) were obtained by solvent precipitation with acetonitrile, and stabilized by reversible homo-bifunctional crosslinking to accomplish a Cyt-c-based drug delivery system that combines stimulus-responsive release and active targeting. Cyt c was released under intracellular redox conditions, due to an S–S bond in the NPs linker, while NPs remained intact without any release under extracellular conditions. The NP surface was decorated with a hydrophilic folic acid–polyethylene glycol (FA–PEG) polymer for active targeting. The FA-decorated NPs specifically recognized and killed cancer cells (IC50 = 47.46 µg/mL) that overexpressed FR, but showed no toxicity against FR-negative cells. Confocal microscopy confirmed the preferential uptake and apoptosis induction of our NPs by FR-positive cancer cells. In vivo experiments using a Lewis lung carcinoma (LLC) mouse model showed visible NP accumulation within the tumor and inhibited the growth of LLC tumors.
Collapse
|
13
|
Folate-Decorated Cross-Linked Cytochrome c Nanoparticles for Active Targeting of Non-Small Cell Lung Carcinoma (NSCLC). Pharmaceutics 2022; 14:pharmaceutics14030490. [PMID: 35335867 PMCID: PMC8951294 DOI: 10.3390/pharmaceutics14030490] [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: 01/08/2022] [Revised: 02/16/2022] [Accepted: 02/20/2022] [Indexed: 01/27/2023] Open
Abstract
The folate receptor alpha (FR), which is overexpressed in solid tumors including NSCLC, can be utilized for active tumor targeting to afford more effective cancer therapies. In this context, cytochrome c (Cyt c) has drawn attention to cancer research because it is non-toxic, yet, when delivered to the cytoplasm of cancer cells, can kill them by inducing apoptosis. Cyt c nanoparticles (NPs, 169 ± 9 nm) were obtained by solvent precipitation with acetonitrile, and stabilized by reversible homo-bifunctional crosslinking to accomplish a Cyt-c-based drug delivery system that combines stimulus-responsive release and active targeting. Cyt c was released under intracellular redox conditions, due to an S–S bond in the NPs linker, while NPs remained intact without any release under extracellular conditions. The NP surface was decorated with a hydrophilic folic acid–polyethylene glycol (FA–PEG) polymer for active targeting. The FA-decorated NPs specifically recognized and killed cancer cells (IC50 = 47.46 µg/mL) that overexpressed FR, but showed no toxicity against FR-negative cells. Confocal microscopy confirmed the preferential uptake and apoptosis induction of our NPs by FR-positive cancer cells. In vivo experiments using a Lewis lung carcinoma (LLC) mouse model showed visible NP accumulation within the tumor and inhibited the growth of LLC tumors.
Collapse
|
14
|
Dominguez-Martinez I, Joaquin-Ovalle F, Ferrer-Acosta Y, Griebenow KH. Folate-Decorated Cross-Linked Cytochrome c Nanoparticles for Active Targeting of Non-Small Cell Lung Carcinoma (NSCLC). Pharmaceutics 2022. [DOI: https:/doi.org/10.3390/pharmaceutics14030490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The folate receptor alpha (FR), which is overexpressed in solid tumors including NSCLC, can be utilized for active tumor targeting to afford more effective cancer therapies. In this context, cytochrome c (Cyt c) has drawn attention to cancer research because it is non-toxic, yet, when delivered to the cytoplasm of cancer cells, can kill them by inducing apoptosis. Cyt c nanoparticles (NPs, 169 ± 9 nm) were obtained by solvent precipitation with acetonitrile, and stabilized by reversible homo-bifunctional crosslinking to accomplish a Cyt-c-based drug delivery system that combines stimulus-responsive release and active targeting. Cyt c was released under intracellular redox conditions, due to an S–S bond in the NPs linker, while NPs remained intact without any release under extracellular conditions. The NP surface was decorated with a hydrophilic folic acid–polyethylene glycol (FA–PEG) polymer for active targeting. The FA-decorated NPs specifically recognized and killed cancer cells (IC50 = 47.46 µg/mL) that overexpressed FR, but showed no toxicity against FR-negative cells. Confocal microscopy confirmed the preferential uptake and apoptosis induction of our NPs by FR-positive cancer cells. In vivo experiments using a Lewis lung carcinoma (LLC) mouse model showed visible NP accumulation within the tumor and inhibited the growth of LLC tumors.
Collapse
|
15
|
Oncogenic KRAS promotes growth of lung cancer cells expressing SLC3A2-NRG1 fusion via ADAM17-mediated shedding of NRG1. Oncogene 2022; 41:280-292. [PMID: 34743207 DOI: 10.1038/s41388-021-02097-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 09/27/2021] [Accepted: 10/25/2021] [Indexed: 12/27/2022]
Abstract
We previously found the SLC3A2-NRG1 (S-N) fusion gene in a lung adenocarcinoma specimen without known driver mutations and validated this in 59 invasive mucinous adenocarcinoma (IMA) samples. Interestingly, KRAS mutation coexisted (62.5%) in 10 out of 16 NRG1 fusions. In this study, we examined the role of mutant KRAS in regulating the S-N fusion protein in KRAS mutant (H358) and wild-type (Calu-3) cells. KRAS mutation-mediated increase in MEK1/2 and ERK1/2 activity enhanced disintegrin and metalloproteinase (ADAM)17 activity, which increased the shedding of NRG1 from the S-N fusion protein. The cleavage of NRG1 also increased the phosphorylation of ERBB2-ERBB3 heterocomplex receptors and their downstream signalling pathways, including PI3K/Akt/mTOR, even under activated KRAS mutation signalling. The concurrence of S-N fusion and KRAS mutation synergistically increased cell proliferation, colony formation, tumour growth, and the cells' resistance to EGFR kinase inhibitors more than KRAS mutation alone. Targeted inhibition of MEK1/2, and ADAM17 significantly induced apoptosis singly and when combined with each mutation singly or with chemotherapy in both the concurrent KRAS mutant and S-N fusion xenograft and lung orthotopic models. Taken together, this is the first study to report that KRAS mutation increased NRG1 cleavage from the S-N fusion protein through ADAM17, thereby enhancing the Ras/Raf/MEK/ERK and ERBB/PI3K/Akt/mTOR pathways. Moreover, the coexistence of KRAS mutant and S-N fusion in lung tumours renders them vulnerable to MEK1/2 and/or ADAM17 inhibitors, at least in part, due to their dependency on the strong positive loop between KRAS mutation and S-N fusion.
Collapse
|
16
|
Hijazo-Pechero S, Alay A, Marín R, Vilariño N, Muñoz-Pinedo C, Villanueva A, Santamaría D, Nadal E, Solé X. Gene Expression Profiling as a Potential Tool for Precision Oncology in Non-Small Cell Lung Cancer. Cancers (Basel) 2021; 13:4734. [PMID: 34638221 PMCID: PMC8507534 DOI: 10.3390/cancers13194734] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 01/20/2023] Open
Abstract
Recent technological advances and the application of high-throughput mutation and transcriptome analyses have improved our understanding of cancer diseases, including non-small cell lung cancer. For instance, genomic profiling has allowed the identification of mutational events which can be treated with specific agents. However, detection of DNA alterations does not fully recapitulate the complexity of the disease and it does not allow selection of patients that benefit from chemo- or immunotherapy. In this context, transcriptional profiling has emerged as a promising tool for patient stratification and treatment guidance. For instance, transcriptional profiling has proven to be especially useful in the context of acquired resistance to targeted therapies and patients lacking targetable genomic alterations. Moreover, the comprehensive characterization of the expression level of the different pathways and genes involved in tumor progression is likely to better predict clinical benefit from different treatments than single biomarkers such as PD-L1 or tumor mutational burden in the case of immunotherapy. However, intrinsic technical and analytical limitations have hindered the use of these expression signatures in the clinical setting. In this review, we will focus on the data reported on molecular classification of non-small cell lung cancer and discuss the potential of transcriptional profiling as a predictor of survival and as a patient stratification tool to further personalize treatments.
Collapse
Affiliation(s)
- Sara Hijazo-Pechero
- Unit of Bioinformatics for Precision Oncology, Catalan Institute of Oncology (ICO), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (S.H.-P.); (A.A.); (R.M.)
- Preclinical and Experimental Research in Thoracic Tumors (PrETT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (N.V.); (C.M.-P.)
| | - Ania Alay
- Unit of Bioinformatics for Precision Oncology, Catalan Institute of Oncology (ICO), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (S.H.-P.); (A.A.); (R.M.)
- Preclinical and Experimental Research in Thoracic Tumors (PrETT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (N.V.); (C.M.-P.)
| | - Raúl Marín
- Unit of Bioinformatics for Precision Oncology, Catalan Institute of Oncology (ICO), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (S.H.-P.); (A.A.); (R.M.)
- Preclinical and Experimental Research in Thoracic Tumors (PrETT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (N.V.); (C.M.-P.)
| | - Noelia Vilariño
- Preclinical and Experimental Research in Thoracic Tumors (PrETT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (N.V.); (C.M.-P.)
- Thoracic Oncology Unit, Department of Medical Oncology, Catalan Institute of Oncology (ICO), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Neuro-Oncology Unit, Hospital Universitari de Bellvitge-ICO L’Hospitalet (IDIBELL), 08908 Barcelona, Spain
| | - Cristina Muñoz-Pinedo
- Preclinical and Experimental Research in Thoracic Tumors (PrETT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (N.V.); (C.M.-P.)
| | - Alberto Villanueva
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain;
| | - David Santamaría
- INSERM U1218, ACTION Laboratory, Institut Européen de Chimie et Biologie (IECB), Université de Bordeaux, F-33607 Pessac, France;
| | - Ernest Nadal
- Preclinical and Experimental Research in Thoracic Tumors (PrETT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (N.V.); (C.M.-P.)
- Thoracic Oncology Unit, Department of Medical Oncology, Catalan Institute of Oncology (ICO), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Xavier Solé
- Unit of Bioinformatics for Precision Oncology, Catalan Institute of Oncology (ICO), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (S.H.-P.); (A.A.); (R.M.)
- Preclinical and Experimental Research in Thoracic Tumors (PrETT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (N.V.); (C.M.-P.)
- CIBER (Consorcio de Investigación Biomédica en Red) Epidemiologia y Salud Pública (CIBERESP), 28029 Madrid, Spain
| |
Collapse
|
17
|
Wang X, Zhou B, Xia Y, Zuo J, Liu Y, Bi X, Luo X, Zhang C. A methylation-based nomogram for predicting survival in patients with lung adenocarcinoma. BMC Cancer 2021; 21:801. [PMID: 34247575 PMCID: PMC8273993 DOI: 10.1186/s12885-021-08539-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 06/28/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND DNA methylation alteration is frequently observed in Lung adenocarcinoma (LUAD) and may play important roles in carcinogenesis, diagnosis, and prognosis. Thus, this study aimed to construct a reliable methylation-based nomogram, guiding prognostic classification screening and personalized medicine for LUAD patients. METHOD The DNA methylation data, gene expression data and corresponding clinical information of lung adenocarcinoma samples were extracted from The Cancer Genome Atlas (TCGA) database. Differentially methylated sites (DMSs) and differentially expressed genes (DEGs) were obtained and then calculated correlation by pearson correlation coefficient. Functional enrichment analysis and Protein-protein interaction network were used to explore the biological roles of aberrant methylation genes. A prognostic risk score model was constructed using univariate Cox and LASSO analysis and was assessed in an independent cohort. A methylation-based nomogram that included the risk score and the clinical risk factors was developed, which was evaluated by concordance index and calibration curves. RESULT We identified a total of 1362 DMSs corresponding to 471 DEGs with significant negative correlation, including 752 hypermethylation sites and 610 hypomethylation sites. Univariate cox regression analysis showed that 59 DMSs were significantly associated with overall survival. Using LASSO method, we constructed a three-DMSs signature that was independent predictive of prognosis in the training cohort. Patients in high-risk group had a significant shorter overall survival than patients in low-risk group classified by three-DMSs signature (log-rank p = 1.9E-04). Multivariate cox regression analysis proved that the three-DMSs signature was an independent prognostic factor for LUAD in TCGA-LUAD cohort (HR = 2.29, 95%CI: 1.47-3.57, P = 2.36E-04) and GSE56044 cohort (HR = 2.16, 95%CI: 1.19-3.91, P = 0.011). Furthermore, a nomogram, combining the risk score with clinical risk factors, was developed with C-indexes of 0.71 and 0.70 in TCGA-LUAD and GSE56044 respectively. CONCLUSIONS The present study established a robust three-DMSs signature for the prediction of overall survival and further developed a nomogram that could be a clinically available guide for personalized treatment of LUAD patients.
Collapse
Affiliation(s)
- Xuelong Wang
- Department of Thoracic Surgery, Capital Medical University Electric Power Teaching Hospital, Beijing, 100073, China
| | - Bin Zhou
- Department of Thoracic Surgery, Capital Medical University Electric Power Teaching Hospital, Beijing, 100073, China
| | - Yuxin Xia
- Department of emergency, Capital Medical University Electric Power Teaching Hospital, Beijing, 100073, China
| | - Jianxin Zuo
- Department of Thoracic Surgery, Capital Medical University Electric Power Teaching Hospital, Beijing, 100073, China
| | - Yanchao Liu
- Department of Thoracic Surgery, Capital Medical University Electric Power Teaching Hospital, Beijing, 100073, China
| | - Xin Bi
- Department of Thoracic Surgery, Capital Medical University Electric Power Teaching Hospital, Beijing, 100073, China
| | - Xiong Luo
- Department of Internal Medicine, Beijing Nuclear Industry Hospital, Beijing, 100822, China
| | - Chengwei Zhang
- Department of Thoracic Surgery, Capital Medical University Electric Power Teaching Hospital, Beijing, 100073, China.
| |
Collapse
|
18
|
|
19
|
Kara A, Özgür A, Nalbantoğlu S, Karadağ A. DNA repair pathways and their roles in drug resistance for lung adenocarcinoma. Mol Biol Rep 2021; 48:3813-3825. [PMID: 33856604 DOI: 10.1007/s11033-021-06314-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 03/24/2021] [Indexed: 01/24/2023]
Abstract
Lung cancer is the leading cancer type of death rate. The lung adenocarcinoma subtype is responsible for almost half of the total lung cancer deaths. Despite the improvements in cancer treatment in recent years, lung adenocarcinoma patients' overall survival rate remains poor. Immunetherapy and chemotherapy are two of the most widely used options for the treatment of cancer. Although many cancer types initially respond to these treatments, the development of resistance is inevitable. The rapid development of drug resistance mainly characterizes lung adenocarcinoma. Despite being the subject of many studies in recent years, the resistance initiation and progression mechanism is still unclear. In this review, we have examined the role of the primary DNA repair pathways (non-homologous end joining (NHEJ) pathway, homologous-recombinant repair (HR) pathway, base excision repair (BER) pathway, and nucleotide excision repair (NER) pathway and transactivation mechanisms of tumor protein 53 (TP53) in drug resistance development. This review suggests that mentioned pathways have essential roles in developing the resistance against chemotherapy and immunotherapy in lung adenocarcinoma patients.
Collapse
Affiliation(s)
- Altan Kara
- Molecular Oncology Laboratory, Genetic Engineering and Biotechnology Institute, TUBITAK Marmara Research Center, Kocaeli, Turkey.
| | - Aykut Özgür
- Laboratory and Veterinary Health Program, Department of Veterinary Medicine, Artova Vocational School, Tokat Gaziosmanpaşa University, Tokat, Turkey
| | - Sinem Nalbantoğlu
- Molecular Oncology Laboratory, Genetic Engineering and Biotechnology Institute, TUBITAK Marmara Research Center, Kocaeli, Turkey
| | - Abdullah Karadağ
- Molecular Oncology Laboratory, Genetic Engineering and Biotechnology Institute, TUBITAK Marmara Research Center, Kocaeli, Turkey
| |
Collapse
|
20
|
Kim YJ, Oremus M, Chen HH, McFarlane T, Fearon D, Horton S. Factors affecting treatment selection and overall survival for first-line EGFR-tyrosine kinase inhibitor therapy in non-small-cell lung cancer. J Comp Eff Res 2021; 10:193-206. [PMID: 33543641 DOI: 10.2217/cer-2020-0173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Aim: To investigate the factors associated with treatment selection and overall survival for first-line EGFR-tyrosine kinase inhibitors (EGFR-TKIs) therapy among patients with non-small-cell lung cancer. Materials & methods: We conducted a retrospective cohort study of linked administrative health databases in Ontario, Canada. Results: A total of 1011 patients received an EGFR-TKI as first-line therapy. Treatment selection and overall survival associated with these treatments were affected by age, sex, geographical residency, comorbidities and different sites of metastasis. Conclusion: Though recent approval of osimertinib offers a potential new standard of care in the first-line setting, earlier generation TKIs remain pillars in treatment of non-small-cell lung cancer therapeutic armamentarium. Our findings may contribute to optimizing treatment sequencing of EGFR-TKIs to maximize clinical benefits.
Collapse
Affiliation(s)
- Yong-Jin Kim
- School of Public Health & Health Systems, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Mark Oremus
- School of Public Health & Health Systems, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Helen H Chen
- School of Public Health & Health Systems, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Thomas McFarlane
- School of Pharmacy, University of Waterloo, Kitchener, ON N2G 1C5, Canada
| | - Danielle Fearon
- School of Public Health & Health Systems, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Susan Horton
- School of Public Health & Health Systems, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| |
Collapse
|
21
|
Lee J, Ahn MJ. Immune checkpoint inhibitors in driver mutation-positive nonsmall cell lung cancer: is there a role? Curr Opin Oncol 2021; 33:64-72. [PMID: 33186183 DOI: 10.1097/cco.0000000000000698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Despite advances in immunotherapy for nonsmall cell lung cancer patients, the clinical efficacy of drugs for patients with oncogenic driver mutations remains limited. This article aimed to comprehensively review the currently available data on the efficacy and safety of immune checkpoint blockade (ICB) for patients with driver mutation-positive lung cancer. RECENT FINDINGS Despite the positive interaction between activation of oncogenic pathways and upregulated PD-L1 expression demonstrated in preclinical studies, the efficacy of single-agent ICB in patients with oncogenic mutation has largely been discouraging, except for those with KRAS mutations. The combination therapies using ICB with tyrosine kinase inhibitors (TKIs) for EGFR/ALK alteration raised a concern for the high incidence of treatment-related adverse events, notably hepatotoxicity and interstitial lung disease. A novel combination with bevacizumab demonstrated promising efficacy with tolerable safety profiles. SUMMARY Other than patients with the KRAS mutation who demonstrate relatively favorable response to ICB, a single-agent ICB therapy should be considered for those who retain good performance status but have no other therapeutic options available. Further studies on the combination of ICB and TKI are needed to identify the most viable pair regarding safety. Additional studies using novel combination partners, such as anti-VEGF inhibitors, are also warranted.
Collapse
Affiliation(s)
- Jiyun Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | | |
Collapse
|
22
|
Shi S, Xu M, Xi Y. Molecular subtypes based on DNA promoter methylation predict prognosis in lung adenocarcinoma patients. Aging (Albany NY) 2020; 12:23917-23930. [PMID: 33237038 PMCID: PMC7762488 DOI: 10.18632/aging.104062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/25/2020] [Indexed: 04/30/2023]
Abstract
BACKGROUND The heterogeneity of lung adenocarcinoma (LADC) makes the early diagnosis and treatment of the disease difficult. Gene silencing of DNA methylation is an important mechanism of tumorigenesis. A combination of methylation and clinical features can improve the classification of LADC heterogeneity. RESULTS We investigated the prognostic significance of 335 specimen subgroups of Lung adenocarcinoma based on the DNA methylation level. The differences in DNA methylation levels were related to the TNM stage classification, age, gender, and prognostic values. Seven subtypes were determined using 774 CpG sites that significantly affected the survival rate based on the consensus clustering. Finally, we constructed a prognostic model that performed well and further verified it in our test group. CONCLUSIONS This study shows that classification based on DNA methylation might aid in demonstrating heterogeneity within formerly characterized LADC molecular subtypes, assisting in the development of efficient, personalized therapy. METHODS Methylation data of lung adenocarcinoma were downloaded from the University of California Santa Cruz (UCSC) cancer browser, and the clinical patient information and RNA-seq archives were acquired from the Cancer Genome Atlas (TCGA). CpG sites were identified based on the significant correlation with the prognosis and used further to cluster the cases uniformly into several subtypes.
Collapse
Affiliation(s)
- Shanping Shi
- Diabetes Center, Zhejiang Provincial Key Laboratory of Pathophysiology, Institute of Biochemistry and Molecular Biology, School of Medicine, Ningbo University, Ningbo 315211, China
| | - Mingjun Xu
- Diabetes Center, Zhejiang Provincial Key Laboratory of Pathophysiology, Institute of Biochemistry and Molecular Biology, School of Medicine, Ningbo University, Ningbo 315211, China
| | - Yang Xi
- Diabetes Center, Zhejiang Provincial Key Laboratory of Pathophysiology, Institute of Biochemistry and Molecular Biology, School of Medicine, Ningbo University, Ningbo 315211, China
| |
Collapse
|
23
|
Gorbunova AS, Denisenko TV, Yapryntseva MA, Pivnyuk AD, Prikazchikova TA, Gogvadze VG, Zhivotovsky B. BNIP3 as a Regulator of Cisplatin-Induced Apoptosis. BIOCHEMISTRY (MOSCOW) 2020; 85:1245-1253. [PMID: 33202209 DOI: 10.1134/s0006297920100120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
BNIP3 is a member of Bcl-2 protein family involved in regulation of various forms of cell death. However, its role in these processes remains unclear and varies depending on the type of cancer cells and environmental factors (pH, O2 level, etc.). Here, the role of BNIP3 in apoptosis regulation in lung adenocarcinoma cells was investigated. The suppressed expression of BNIP3 caused inhibition of oxygen consumption and stimulated production of the mitochondrial reactive oxygen species, suggesting the role of BNIP3 in induction of mitochondrial dysfunction and its potential involvement in regulation of cell death. Indeed, cytochrome c release in the cells with BNIP3 knockout and knockdown was higher than in the wild-type (WT) upon apoptosis stimulation by cisplatin. Moreover, suppression of BNIP3 expression led to the increase in the caspase-3 activity and, as a consequence, accumulation of the apoptotic marker - p89 fragment of poly(ADP-ribose)-polymerase (PARP) - as compared to WT cells. Analysis of the SubG1 population by flow cytometry confirmed the elevated level of apoptosis in the BNIP3 knockout cells. Pretreatment with the antioxidant Trolox did not affect cell death, indicating that it was independent on reactive oxygen species. These data show that BNIP3 is involved in maintaining normal functioning of mitochondria and, as a result, can regulate the mitochondrial pathway of cell death.
Collapse
Affiliation(s)
- A S Gorbunova
- Faculty of Basic Medicine, Lomonosov Moscow State University, Moscow, 119192, Russia
| | - T V Denisenko
- Faculty of Basic Medicine, Lomonosov Moscow State University, Moscow, 119192, Russia
| | - M A Yapryntseva
- Faculty of Basic Medicine, Lomonosov Moscow State University, Moscow, 119192, Russia
| | - A D Pivnyuk
- Faculty of Basic Medicine, Lomonosov Moscow State University, Moscow, 119192, Russia
| | - T A Prikazchikova
- Skolkovo Institute of Science and Technology, Center of Life Sciences, Moscow, 121205, Russia
| | - V G Gogvadze
- Faculty of Basic Medicine, Lomonosov Moscow State University, Moscow, 119192, Russia.,Institute of Environmental Medicine, Karolinska Institute, Stockholm, SE-171 77, Sweden
| | - B Zhivotovsky
- Faculty of Basic Medicine, Lomonosov Moscow State University, Moscow, 119192, Russia. .,Institute of Environmental Medicine, Karolinska Institute, Stockholm, SE-171 77, Sweden
| |
Collapse
|
24
|
Cui J, Song Y, Han X, Hu J, Chen Y, Chen X, Xu X, Xing Y, Lu H, Cai L. Targeting 14-3-3ζ Overcomes Resistance to Epidermal Growth Factor Receptor-Tyrosine Kinase Inhibitors in Lung Adenocarcinoma via BMP2/Smad/ID1 Signaling. Front Oncol 2020; 10:542007. [PMID: 33123465 PMCID: PMC7571474 DOI: 10.3389/fonc.2020.542007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 08/20/2020] [Indexed: 01/06/2023] Open
Abstract
Background: The 14-3-3ζ protein, which acts as a putative oncoprotein, has been found to promote the proliferation, metastasis, and chemoresistance of cancer cells in several cancers including lung adenocarcinoma (LUAD); however, its significance in epidermal growth factor receptor–tyrosine kinase inhibitor (EGFR-TKI) resistance remains unknown. Methods: The Cancer Genome Atlas (TCGA) database was used to determine 14-3-3ζ expression in pancancer and LUAD. 14-3-3ζ and ID1 expression was then examined in clinical LUAD samples by immunohistochemistry (IHC). Lentiviral transfection with 14-3-3ζ-specific small hairpin RNA (shRNA) was used to establish stable 14-3-3ζ knockdown gefitinib-resistant PC9 (PC9/GR) and H1975 cell lines. The effect of 14-3-3ζ knockdown on reversing EGFR-TKI resistance was determined in vitro by Cell Counting Kit-8 (CCK-8), wound healing, Transwell assays, and flow cytometry. A xenograft tumor model was established to evaluate the role of 14-3-3ζ in EGFR-TKI resistance. Microarray analysis results showed multiple pathways regulated by 14-3-3ζ-shRNA. Results: In the present study, we demonstrated that based on the TCGA, pancancer and LUAD 14-3-3ζ expression was elevated and predicted unfavorable prognosis. In addition, high 14-3-3ζ expression was associated with advanced T stage, TNM stage, presence of lymph node metastasis and, importantly, poor treatment response to EGFR-TKIs in LUAD patients with EGFR-activating mutations. 14-3-3ζ shRNA sensitized EGFR-TKI-resistant human LUAD cells to gefitinib and reversed epithelial-to-mesenchymal transition (EMT). After 14-3-3ζ depletion, bone morphogenetic protein (BMP) signaling activation was decreased in EGFR-TKI-resistant cells in microarray analysis, which was further validated by Western blot analysis. Furthermore, the expression of 14-3-3ζ positively correlates with ID1 expression in human EGFR-mutant LUAD patient samples. In vivo, there was a reduction in the tumor burden in mice treated with 14-3-3ζ shRNA and gefitinib compared to mice treated with gefitinib alone. Conclusion: Our work uncovers a hitherto unappreciated role of 14-3-3ζ in EGFR-TKI resistance. This study might provide a potential therapeutic approach for treating LUAD patients harboring EGFR mutations.
Collapse
Affiliation(s)
- Jinfang Cui
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yang Song
- Department of Orthopedic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xuejiao Han
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jing Hu
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yanbo Chen
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xuesong Chen
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xiaomin Xu
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Ying Xing
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Hailing Lu
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Li Cai
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| |
Collapse
|
25
|
Hua P, Zhang Y, Jin C, Zhang G, Wang B. Integration of gene profile to explore the hub genes of lung adenocarcinoma: A quasi-experimental study. Medicine (Baltimore) 2020; 99:e22727. [PMID: 33120770 PMCID: PMC7581154 DOI: 10.1097/md.0000000000022727] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Lung cancer is a leading cause of morbidity diseases worldwide, but the key mechanisms of lung cancer remain elusive. This study aims to integrate of GSE 118370 and GSE 32863 profile and identify the key genes and pathway involved in human lung adenocarcinoma. METHODS R software (RStudio, Version info: R 3.2.3, Forrester, USA) were utilized to find the differentially expressed genes. All the differentially expressed genes were analyzed by gene ontology, kyoto encyclopedia of genes and genomes. Protein-protein interaction networks were constructed by STRING database and analyzed by Cytohubber and Module. The cancer genome atlas database was used to verification the expression of hub genes. Quantitative reverse transcription-PCR was used to verify the bio-information results. RESULTS Sixty-four lung adenocarcinoma and 64 adjacent normal tissues were used for integration analysis. Five hundred ninety-nine co-expression genes were locked. Biological processes mainly enriched in angiogenesis. Cellular component focused on extracellular exosome and molecular function aimed on protein disulfide isomerase activity. Cytohubber analysis showed that GNG11, FPR2, P4HB, PIK3R1, CDC20, ADCY4, TIMP1, IL6, CXC chemokine ligand (CXCL)12, and GAS6 acted as the hub genes during lung adenocarcinoma. Module analysis presented Chemokine signaling pathway was a key pathway. Quantitative reverse transcription-PCR showed that the expression level of GNG11, FPR2, PIK3R1, ADCY4, IL6, CXCL12, and GAS6 were significantly decreased and P4HB, CDC20 and TIMP1 were increased in human adenocarcinoma tissues (P < .05). The cancer genome atlas online analysis showed GNG11 was not associated with survival. CONCLUSIONS This study firstly reported GNG11 acting as a hub gene in adenocarcinoma. GNG11 could be used as a biomarker for human adenocarcinoma. Chemokine signaling pathway might play important roles in lung adenocarcinoma.
Collapse
|
26
|
Yang Y, Xie X, Jiang G, Liu H. Different driver gene mutations in patients with synchronous multiple primary lung cancers: a case report. J Cardiothorac Surg 2020; 15:196. [PMID: 32727606 PMCID: PMC7389679 DOI: 10.1186/s13019-020-01178-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 06/02/2020] [Indexed: 11/10/2022] Open
Abstract
Background Routine clinical and pathological examinations usually cannot fully conclusively determine the relationship between different lesions of lung cancer. Detailed genetic analysis of tumor samples may supply important additional information and identify second primary lung cancers. Case presentation In the present study, we report a case of synchronous multiple primary lung cancer (MPLC) composed of two distinct pathological subtypes with epidermal growth factor receptor (EGFR) gene mutations L858R of the acinar adenocarcinoma subtype and EML4–ALK rearrangement of the squamous cell carcinoma. Conclusion The present report highlights the clinical importance of molecular cancer biomarkers detection to guide management decisions in MPLC cases.
Collapse
Affiliation(s)
- Yong Yang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, No. 507 Zhengmin Road, Shanghai, 200433, China
| | - Xiaofeng Xie
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Gening Jiang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, No. 507 Zhengmin Road, Shanghai, 200433, China
| | - Hongcheng Liu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, No. 507 Zhengmin Road, Shanghai, 200433, China.
| |
Collapse
|
27
|
Luo H, Zhang T, Cheng P, Li D, Ogorodniitchouk O, Lahmamssi C, Wang G, Lan M. Therapeutic implications of fibroblast growth factor receptor inhibitors in a combination regimen for solid tumors. Oncol Lett 2020; 20:2525-2536. [PMID: 32782571 DOI: 10.3892/ol.2020.11858] [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: 11/22/2019] [Accepted: 05/22/2020] [Indexed: 12/12/2022] Open
Abstract
A number of novel drugs targeting the fibroblast growth factor receptor (FGFR) signaling pathway have been developed, including mostly tyrosine kinase inhibitors, selective inhibitors or monoclonal antibodies. Multiple preclinical and clinical studies have been conducted worldwide to ascertain their effects on diverse solid tumors. Drugs, such as lenvatinib, dovitinib and other non-specific FGFR inhibitors, widely used in clinical practice, have been approved by the Food and Drug Administration for cancer therapy, although the majority of drugs remain in preclinical tests or clinical research. The resistance to a single agent for FGFR inhibition with synthetic lethal action may be overcome by a combination of therapeutic approaches and FGFR inhibitors, which could also enhance the sensitivity to other therapeutics. Therefore, the aim of the present review is to describe the pharmacological characteristics of FGFR inhibitors that may be combined with other therapeutic agents and the preclinical data supporting their combination. Additionally, their clinical implications and the remaining challenges for FGFR inhibitor combination regimens are discussed.
Collapse
Affiliation(s)
- Hong Luo
- Department of Oncology, General Hospital of Western Theater Command, Chengdu, Sichuan 610083, P.R. China
| | - Tao Zhang
- Department of Oncology, General Hospital of Western Theater Command, Chengdu, Sichuan 610083, P.R. China
| | - Peng Cheng
- Department of Oncology, General Hospital of Western Theater Command, Chengdu, Sichuan 610083, P.R. China
| | - Dong Li
- Department of Oncology, General Hospital of Western Theater Command, Chengdu, Sichuan 610083, P.R. China
| | | | - Chaimaa Lahmamssi
- Institut de Cancérologie Lucien Neuwirth, 42270 Saint Priest en Jarez, France
| | - Ge Wang
- Cancer Center, Institute of Surgical Research, Third Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing 400042, P.R. China
| | - Meiling Lan
- Cancer Center, The Third Affiliated Hospital of Chongqing Medical University (Jie Er Hospital), Chongqing 401120, P.R. China
| |
Collapse
|
28
|
Gao Y, Luo L, Xie Y, Zhao Y, Yao J, Liu X. PYCR1 knockdown inhibits the proliferation, migration, and invasion by affecting JAK/STAT signaling pathway in lung adenocarcinoma. Mol Carcinog 2020; 59:503-511. [PMID: 32133692 DOI: 10.1002/mc.23174] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 02/21/2020] [Accepted: 02/21/2020] [Indexed: 12/14/2022]
Abstract
Lung adenocarcinoma (LUAD), as a form of non-small cell lung cancer (NSCLC), is the most frequently diagnosed lung cancer worldwide. To date, a few biomarkers have been reported to provide valuable information in guiding LUAD treatment. The aim of our study was to explore the functional role of pyrroline-5-carboxylate reductase 1 (PYCR1) in LUAD. Based on Oncomine database, we found that PYCR1 was highly expressed in LUAD tissues. We also confirmed an abnormal increase of PYCR1 expression in LUAD cell lines and patients' tissues. Through Kaplan-Meier plotter database, we further studied the prognostic values of PYCR1. The outcomes indicated that overexpressed PYCR1 associated with poor prognosis among LUAD patients. To further study the function of PYCR1 in LUAD, cell counting kit-8, colony-forming, scratch wound healing, and Transwell assays were conducted. The results suggested that knockdown of PYCR1 curbed cell proliferation, migration, and invasion in LUAD cell lines. Subsequently, we identified 50 top genes positively and negatively correlated with PYCR1 in LUAD, and conducted biological pathway enrichment analysis of these genes. Among those enriched pathways, we selected JAK/STAT signaling pathway for further analysis. The results of Western blot assays revealed that PYCR1 knockdown significantly increased the expression of Bcl-2 and c-Myc, and the phosphorylation level of JAK2 and STAT3. Taken together, this study unearthed that PYCR1 knockdown could inhibit tumor growth and affect the JAK/STAT signaling pathway in LUAD. This study may contribute to a better understanding of PYCR1 in LUAD and provide a potential biomarker for cancer prognosis.
Collapse
Affiliation(s)
- Yawen Gao
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Lihua Luo
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Yangchun Xie
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Yu Zhao
- Rochester Regional Health/Unity Hospital, Rochester, New York
| | - Jie Yao
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Xianling Liu
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| |
Collapse
|
29
|
Chavdoula E, Habiel DM, Roupakia E, Markopoulos GS, Vasilaki E, Kokkalis A, Polyzos AP, Boleti H, Thanos D, Klinakis A, Kolettas E, Marcu KB. CHUK/IKK-α loss in lung epithelial cells enhances NSCLC growth associated with HIF up-regulation. Life Sci Alliance 2019; 2:2/6/e201900460. [PMID: 31792060 PMCID: PMC6892436 DOI: 10.26508/lsa.201900460] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 02/06/2023] Open
Abstract
IKKα is an NSCLC suppressor and its loss in mouse AT-II lung epithelial cells or in human NSCLC lines increased urethane-induced adenoma growth and xenograft burdens, respectively. IKKα loss can up-regulate HIF-1α, enhancing tumor growth under hypoxia. Through the progressive accumulation of genetic and epigenetic alterations in cellular physiology, non–small-cell lung cancer (NSCLC) evolves in distinct steps involving mutually exclusive oncogenic mutations in K-Ras or EGFR along with inactivating mutations in the p53 tumor suppressor. Herein, we show two independent in vivo lung cancer models in which CHUK/IKK-α acts as a major NSCLC tumor suppressor. In a novel transgenic mouse strain, wherein IKKα ablation is induced by tamoxifen (Tmx) solely in alveolar type II (AT-II) lung epithelial cells, IKKα loss increases the number and size of lung adenomas in response to the chemical carcinogen urethane, whereas IKK-β instead acts as a tumor promoter in this same context. IKKα knockdown in three independent human NSCLC lines (independent of K-Ras or p53 status) enhances their growth as tumor xenografts in immune-compromised mice. Bioinformatics analysis of whole transcriptome profiling followed by quantitative protein and targeted gene expression validation experiments reveals that IKKα loss can result in the up-regulation of activated HIF-1-α protein to enhance NSCLC tumor growth under hypoxic conditions in vivo.
Collapse
Affiliation(s)
- Evangelia Chavdoula
- Biomedical Research Foundation Academy of Athens, Athens, Greece.,Laboratory of Biology, School of Medicine, Faculty of Health Sciences, University of Ioannina, University Campus, Ioannina, Greece.,Biomedical Research Division, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Ioannina, Greece
| | | | - Eugenia Roupakia
- Laboratory of Biology, School of Medicine, Faculty of Health Sciences, University of Ioannina, University Campus, Ioannina, Greece.,Biomedical Research Division, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Ioannina, Greece
| | - Georgios S Markopoulos
- Laboratory of Biology, School of Medicine, Faculty of Health Sciences, University of Ioannina, University Campus, Ioannina, Greece.,Biomedical Research Division, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Ioannina, Greece
| | - Eleni Vasilaki
- Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Antonis Kokkalis
- Biomedical Research Foundation Academy of Athens, Athens, Greece
| | | | - Haralabia Boleti
- Intracellular Parasitism Laboratory, Department of Microbiology and Light Microscopy Unit, Hellenic Pasteur Institute, Athens, Greece
| | - Dimitris Thanos
- Biomedical Research Foundation Academy of Athens, Athens, Greece
| | | | - Evangelos Kolettas
- Laboratory of Biology, School of Medicine, Faculty of Health Sciences, University of Ioannina, University Campus, Ioannina, Greece .,Biomedical Research Division, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Ioannina, Greece
| | - Kenneth B Marcu
- Biomedical Research Foundation Academy of Athens, Athens, Greece .,Laboratory of Biology, School of Medicine, Faculty of Health Sciences, University of Ioannina, University Campus, Ioannina, Greece.,Biomedical Research Division, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Ioannina, Greece.,Departments of Biochemistry and Cell Biology and Pathology, Stony Brook University, Stony Brook, NY, USA.,Department of Biological Sciences, San Diego State University, San Diego, CA, USA
| |
Collapse
|
30
|
Wang R, Zhu H, Yang M, Zhu C. DNA methylation profiling analysis identifies a DNA methylation signature for predicting prognosis and recurrence of lung adenocarcinoma. Oncol Lett 2019; 18:5831-5842. [PMID: 31788056 PMCID: PMC6865134 DOI: 10.3892/ol.2019.10931] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 08/16/2019] [Indexed: 12/12/2022] Open
Abstract
The aim of the present study was to identify candidate prognostic DNA methylation biomarkers for lung adenocarcinoma (LUAD), since the modern precise medicine for the treatment of LUAD requires more biomarkers and novel therapeutic targets of interest. DNA methylation profiling data of LUAD were downloaded from The Cancer Gene Atlas portal. Differentially methylated genes (DMGs) were screened to differentiate between samples designated as good and bad prognosis. LUAD-associated methylation modules were obtained with the weighted correlation network analysis (WGCNA) package, followed by function enrichment analysis. Optimal prognostic DMGs were selected using the LASSO estimation-based Cox-PH approach and were used to construct a prognostic risk scoring system. The training set was dichotomized by risk score, into high- and low-risk groups. The differences in overall survival (OS) time or recurrence-free survival (RFS) time between the two groups were evaluated using a Kaplan-Meier curve. A total of 742 DMG samples were screened for good and bad prognosis. WGCNA identified three LUAD-associated modules, which were primarily associated with cytoskeleton organization, transcription and apoptosis. A nine-gene prognostic methylation signature was determined, which included C20orf56, BTG2, C13orf16, DNASE1L1, ZDHHC3, FHDC1, ARF6, ITGB3 and ICAM4. A risk score-based methylation signature classified the patients in the training set into high- and low-risk groups with significantly different OS or RFS times. The prognostic value of the methylation signature was successfully verified in a validation set. In conclusion, the present study identified a nine-gene methylation signature for the prediction of survival and recurrence in patients with LUAD and improved the understanding of the alterations in DNA methylation in LUAD.
Collapse
Affiliation(s)
- Rui Wang
- Department of Oncology, Anhui Chest Hospital, Hefei, Anhui 230022, P.R. China
| | - Hong Zhu
- Department of Internal Medicine Oncology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Mingxia Yang
- Department of Pulmonary and Critical Care Medicine, The Affiliated Changzhou No. 2 People's Hospital, Changzhou, Jiangsu 213002, P.R. China
| | - Chunrong Zhu
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| |
Collapse
|
31
|
Hong BJ, Park WY, Kim HR, Moon JW, Lee HY, Park JH, Kim SK, Oh Y, Roe JS, Kim MY. Oncogenic KRAS Sensitizes Lung Adenocarcinoma to GSK-J4-Induced Metabolic and Oxidative Stress. Cancer Res 2019; 79:5849-5859. [PMID: 31506334 DOI: 10.1158/0008-5472.can-18-3511] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 07/29/2019] [Accepted: 09/06/2019] [Indexed: 11/16/2022]
Abstract
Genetic and epigenetic changes (e.g., histone methylation) contribute to cancer development and progression, but our understanding of whether and how specific mutations affect a cancer's sensitivity to histone demethylase (KDM) inhibitors is limited. Here, we evaluated the effects of a panel of KDM inhibitors on lung adenocarcinomas (LuAC) with various mutations. Notably, LuAC lines harboring KRAS mutations showed hypersensitivity to the histone H3K27 demethylase inhibitor GSK-J4. Specifically, GSK-J4 treatment of KRAS mutant-containing LuAC downregulated cell-cycle progression genes with increased H3K27me3. In addition, GSK-J4 upregulated expression of genes involved in glutamine/glutamate transport and metabolism. In line with this, GSK-J4 reduced cellular levels of glutamate, a key source of the TCA cycle intermediate α-ketoglutarate (αKG) and of the antioxidant glutathione, leading to reduced cell viability. Supplementation with an αKG analogue or glutathione protected KRAS-mutant LuAC cells from GSK-J4-mediated reductions in viability, suggesting GSK-J4 exerts its anticancer effects by inducing metabolic and oxidative stress. Importantly, KRAS knockdown in mutant LuAC lines prevented GSK-J4-induced decrease in glutamate levels and reduced their susceptibility to GSK-J4, whereas overexpression of oncogenic KRAS in wild-type LuAC lines sensitized them to GSK-J4. Collectively, our study uncovers a novel association between a genetic mutation and KDM inhibitor sensitivity and identifies the underlying mechanisms. This suggests GSK-J4 as a potential treatment option for cancer patients with KRAS mutations. SIGNIFICANCE: This study not only provides a novel association between KRAS mutation and GSK-J4 sensitivity but also demonstrates the underlying mechanisms, suggesting a potential use of GSK-J4 in cancer patients with KRAS mutations.
Collapse
Affiliation(s)
- Beom-Jin Hong
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Woo-Yong Park
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Hwa-Ryeon Kim
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | - Jin Woo Moon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | | | - Jun Hyung Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Seon-Kyu Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, South Korea
| | - Youngbin Oh
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Jae-Seok Roe
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea.
| | - Mi-Young Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea. .,KAIST Institute for the BioCentury, Cancer Metastasis Control Center, Daejeon, South Korea
| |
Collapse
|
32
|
Ji Z, Pan X, Shang Y, Ni DT, Wu FL. KIF18B as a regulator in microtubule movement accelerates tumor progression and triggers poor outcome in lung adenocarcinoma. Tissue Cell 2019; 61:44-50. [PMID: 31759406 DOI: 10.1016/j.tice.2019.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/01/2019] [Accepted: 09/01/2019] [Indexed: 12/24/2022]
Abstract
KIF18B is involved in several tumor progression and exerts critical effects on microtubule growth during mitosis, but its role in lung adenocarcinoma still remains rare. Hence, we attempted to explore the biological function of KIF18B in lung adenocarcinoma. We first analyzed the expressional pattern of KIF18B in lung adenocarcinoma, and detected the correlation between KIF18B expression and clinical characteristics in lung adenocarcinoma based on The Cancer Genome Atlas (TCGA) database and Oncomine dataset. Subsequently, cell counting kit-8 (CCK-8) assay, wound-healing analysis, and transwell method were performed to assess the effects of KIF18B in lung adenocarcinoma cells. Quantitative real-time reverse transcription-PCR (qRT-PCR) and western blotting were utilized to measure the mRNA and protein expression levels. Our results illustrated that KIF18B expression was significantly up-regulated in lung adenocarcinoma samples compared to normal specimens. High levels of KIF18B were associated with unfavorable prognosis of lung adenocarcinoma patients. Down-regulation of KIF18B in lung adenocarcinoma cells inhibited cell prolifartion, migration, and invasion. Western blot assay demonstrated that KIF18B knockdown markedly decreased Rac1-GTP expression, an important marker of migration and invasion in tumors. Moreover, the phosphorylation of AKT and mTOR expression levels were attenuated after KIF18B knockdown. Taken together, these data enhanced the point that KIF18B might promote lung adenocarcinoma cell proliferation, migration, and invasion by activating Rac1 and mediating the AKT/mTOR signaling pathway.
Collapse
Affiliation(s)
- Ze Ji
- Department of Respiratory Medicine, Suzhou Kowloon Hospital, Shanghai Jiaotong University School of Medicine, Suzhou, Jiangsu, 215028, PR China
| | - Xing Pan
- Department of Nursing, Suzhou Kowloon Hospital, Shanghai Jiaotong University School of Medicine, Suzhou, Jiangsu, 215028, PR China
| | - Yan Shang
- Department of Respiratory and Critical Care Medicine, Changhai Hospital, Second Military Medical University, Shanghai, 200433, PR China
| | - Dian-Tao Ni
- Department of Respiratory Medicine, Suzhou Kowloon Hospital, Shanghai Jiaotong University School of Medicine, Suzhou, Jiangsu, 215028, PR China.
| | - Feng-Lei Wu
- Department of Oncology, First People Hospital of Lianyungang, Lianyungang, Jiangsu, 222002, PR China.
| |
Collapse
|
33
|
Weng CF, Chen PJ, Tseng AH, Huang SH, Lee HHC. Unusual synchronous double primary treatment-naïve lung adenocarcinoma harboring T790M and L858R mutations in early-stage lung cancer. World J Surg Oncol 2019; 17:148. [PMID: 31426797 PMCID: PMC6701136 DOI: 10.1186/s12957-019-1688-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 08/06/2019] [Indexed: 12/14/2022] Open
Abstract
Background Concurrent mutations of synchronous multiple primary non-small cell lung cancer (SMPNSCLC) is rare, and only a few cases have been reported. Herein, we present a case of early-stage SMPNSCLC with T790M and L858R mutations. Case presentation A 68-year-old male patient presented to the Thoracic Surgery Department due to a tumor in the right lower lung. The tumor was detected more than 5 years previously during a health examination; however, the patient ignored the problem because the clinician at that time stated that the lesion was highly likely to be benign. Chest computed topography (CT) was ordered and the images showed a well-defined tumor in the right lower lung and a faint nodular lesion over the left lower lung field. A CT-guided biopsy results showed the presence of atypical cells and positive staining of TTF-1 and CK7. Surgical intervention was performed. The right- and left-sided tumors disclosed micropapillary predominant adenocarcinoma and acinar-predominant adenocarcinoma, respectively. Both tumors were positive for TTF-1 but negative for ALK and p40. Real-time PCR analysis showed that the right-sided tumor had an epidermal growth factor receptor (EGFR) mutation presenting as point mutation T790M in exon 20, while the left-sided tumor had a point mutation L858R in exon 21 of EGFR. Conclusions Our patient’s case suggests that tumors resembling a benign pattern with central calcification may be misdiagnosed. Thus, early screening for lung cancer is important, and intensive efforts to make a diagnosis through surgical resection or biopsies to allow for tailored optimal treatment may be preferential for the best patient outcomes.
Collapse
Affiliation(s)
- Ching-Fu Weng
- Department of Thoracic Medicine, Hsinchu Cathay General Hospital, Hsinchu, Taiwan
| | - Po-Ju Chen
- Department of Thoracic Surgery, Xizhi Cathay General Hospital, New Taipei, Taiwan
| | - Ailun Heather Tseng
- Systems Biology and Bioinformatics, National Central University, Taoyuan, Taiwan
| | - Shih-Hung Huang
- Department of Pathology, Cathay General Hospital, No. 280, Sec. 4, Ren'ai Rd., Da'an Dist., 106, Taipei, Taiwan.
| | - Henry Hsin-Chung Lee
- Department of Surgery, Hsinchu Cathay General Hospital, No. 678, Sec. 2, Zhonghua Rd., East Dist., Hsinchu City, 300, Taiwan.
| |
Collapse
|
34
|
Savage SR, Shi Z, Liao Y, Zhang B. Graph Algorithms for Condensing and Consolidating Gene Set Analysis Results. Mol Cell Proteomics 2019; 18:S141-S152. [PMID: 31142576 PMCID: PMC6692773 DOI: 10.1074/mcp.tir118.001263] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 03/22/2019] [Indexed: 01/04/2023] Open
Abstract
Gene set analysis plays a critical role in the functional interpretation of omics data. Although this is typically done for one omics experiment at a time, there is an increasing need to combine gene set analysis results from multiple experiments performed on the same or different omics platforms, such as in multi-omics studies. Integrating results from multiple experiments is challenging, and annotation redundancy between gene sets further obscures clear conclusions. We propose to use a weighted set cover algorithm to reduce redundancy of gene sets identified in a single experiment. Next, we use affinity propagation to consolidate similar gene sets identified from multiple experiments into clusters and to automatically determine the most representative gene set for each cluster. Using three examples from over representation analysis and gene set enrichment analysis, we showed that weighted set cover outperformed a previously published set cover method and reduced the number of gene sets by 52-77%. Focusing on overlapping genes between the list of input genes and the enriched gene sets in over-representation analysis and leading-edge genes in gene set enrichment analysis further reduced the number of gene sets. A use case combining enrichment analysis results from RNA-Seq and proteomics data comparing basal and luminal A breast cancer samples highlighted the known difference in proliferation and DNA damage response. Finally, we used these algorithms for a pan-cancer survival analysis. Our analysis clearly revealed prognosis-related pathways common to multiple cancer types or specific to individual cancer types, as well as pathways associated with prognosis in different directions in different cancer types. We implemented these two algorithms in an R package, Sumer, which generates tables and static and interactive plots for exploration and publication. Sumer is publicly available at https://github.com/bzhanglab/sumer.
Collapse
Affiliation(s)
- Sara R Savage
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Zhiao Shi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Yuxing Liao
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.
| |
Collapse
|
35
|
He C, He Y, Luo H, Zhang M, Wu J, He X, Fu Y, Chen W, Zou J. Cytoplasmic ERβ1 expression is associated with survival of patients with Stage IV lung adenocarcinoma and an EGFR mutation at exon 21 L858R subsequent to treatment with EGFR-TKIs. Oncol Lett 2019; 18:792-803. [PMID: 31289556 PMCID: PMC6540184 DOI: 10.3892/ol.2019.10348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 02/27/2019] [Indexed: 12/14/2022] Open
Abstract
The present study assessed whether estrogen receptor (ER)β1 is associated with the survival of patients with advanced lung adenocarcinoma, with or without mutations of the epidermal growth factor receptor (EGFR) following treatment with EGFR-tyrosine kinase inhibitors (TKIs). Pathologically confirmed stage IV lung adenocarcinomas were assessed for EGFR mutations and ERβ1 expression. Progression-free survival (PFS) and overall survival (OS) were estimated using the Kaplan-Meier method and the log-rank test. A total of 122 out of the 201 (60.7%) patients had EGFR mutations, 64 (31.8%) of which were EGFR Del19 and 58 mutations (28.9%) were EGFR exon 21 L858R mutation. The presence of EGFR mutations was significantly increased in female patients compared with male patients (P<0.001) and in non-smokers compared with smokers (P<0.001). Patients with EGFR mutations had a significantly improved PFS and OS compared with patients without EGFR mutations treated with EGFR-TKIs. Furthermore, ERβ1 expression was significantly increased in patients with EGFR mutations compared with patients without EGFR mutations (P=0.001). However, the median PFS (P=0.005) and OS (P=0.002) of patients carrying the EGFR exon 21 L858R mutation was significantly decreased in patients with tumors where ERβ1 cytoplasmic expression was high. The multivariate analysis demonstrated that ERβ1 expression was the only independent predictor of PFS (P=0.002) and OS (P=0.003) in patients carrying the EGFR exon 21 L858R mutation. The data demonstrated that ERβ1 expression may predict outcomes of patients with lung adenocarcinoma treated with EGFR-TKI.
Collapse
Affiliation(s)
- Cheng He
- Department of Medical Oncology, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, Anhui 230000, P.R. China.,Department of Thoracic Oncology, Anhui Provincial Cancer Hospital, Hefei, Anhui 230000, P.R. China
| | - Yifu He
- Department of Medical Oncology, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, Anhui 230000, P.R. China.,Department of Medical Oncology, Anhui Provincial Cancer Hospital, Hefei, Anhui 230000, P.R. China
| | - Huiqin Luo
- Department of Medical Oncology, Anhui Provincial Cancer Hospital, Hefei, Anhui 230000, P.R. China
| | - Ming Zhang
- Department of Pathology, Anhui Provincial Cancer Hospital, Hefei, Anhui 230000, P.R. China
| | - Jing Wu
- Department of Pathology, Anhui Provincial Cancer Hospital, Hefei, Anhui 230000, P.R. China
| | - Xiaofang He
- Department of Medical Oncology, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, Anhui 230000, P.R. China
| | - Yuying Fu
- Department of Medical Oncology, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, Anhui 230000, P.R. China
| | - Wenju Chen
- Department of Medical Oncology, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, Anhui 230000, P.R. China
| | - Jinkun Zou
- Department of Medical Oncology, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, Anhui 230000, P.R. China
| |
Collapse
|
36
|
Zhang W, Wang SL. An Integrated Framework for Identifying Mutated Driver Pathway and Cancer Progression. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019; 16:455-464. [PMID: 29990286 DOI: 10.1109/tcbb.2017.2788016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Next-generation sequencing (NGS) technologies provide amount of somatic mutation data in a large number of patients. The identification of mutated driver pathway and cancer progression from these data is a challenging task because of the heterogeneity of interpatient. In addition, cancer progression at the pathway level has been proved to be more reasonable than at the gene level. In this paper, we introduce an integrated framework to identify mutated driver pathways and cancer progression (iMDPCP) at the pathway level from somatic mutation data. First, we use uncertainty coefficient to quantify mutual exclusivity on gene driver pathways and develop a computational framework to identify mutated driver pathways based on the adaptive discrete differential evolution algorithm. Then, we construct cancer progression model for driver pathways based on the Bayesian Network. Finally, we evaluate the performance of iMDPCP on real cancer somatic mutation datasets. The experimental results indicate that iMDPCP is more accurate than state-of-the-art methods according to the enrichment of KEGG pathways, and it also provides new insights on identifying cancer progression at the pathway level.
Collapse
|
37
|
Yi M, Zhu R, Stephens RM. GradientScanSurv-An exhaustive association test method for gene expression data with censored survival outcome. PLoS One 2018; 13:e0207590. [PMID: 30517129 PMCID: PMC6281197 DOI: 10.1371/journal.pone.0207590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 11/03/2018] [Indexed: 12/22/2022] Open
Abstract
Accurate assessment of the association between continuous variables such as gene expression and survival is a critical aspect of precision medicine. In this report, we provide a review of some of the available survival analysis and validation tools by referencing published studies that have utilized these tools. We have identified pitfalls associated with the assumptions inherent in those applications that have the potential to impact scientific research through their potential bias. In order to overcome these pitfalls, we have developed a novel method that enables the logrank test method to handle continuous variables that comprehensively evaluates survival association with derived aggregate statistics. This is accomplished by exhaustively considering all the cutpoints across the full expression gradient. Direct side-by-side comparisons, global ROC analysis, and evaluation of the ability to capture relevant biological themes based on current understanding of RAS biology all demonstrated that the new method shows better consistency between multiple datasets of the same disease, better reproducibility and robustness, and better detection power to uncover biological relevance within the selected datasets over the available survival analysis methods on univariate gene expression and penalized linear model-based methods.
Collapse
Affiliation(s)
- Ming Yi
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States of America
- * E-mail:
| | - Ruoqing Zhu
- Department of Statistics, University of Illinois Urbana-Champaign, Champaign, IL, United States of America
| | - Robert M. Stephens
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States of America
| |
Collapse
|
38
|
Estêvão D, Rios Costa N, da Costa RG, Medeiros R. CRISPR-Cas9 therapies in experimental mouse models of cancer. Future Oncol 2018; 14:2083-2095. [PMID: 30027767 DOI: 10.2217/fon-2018-0028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The CRISPR-Cas9, a part of the defence mechanism from bacteria, has rapidly become the simplest, fastest and the most precise genome-editing tool available. The therapeutic applications of CRISPR are boundless: correction of mutations in several disorders, inactivation of oncogenes and viral oncoproteins, and activation of tumor suppressor genes. In this review, we expose recent advances concerning animal models of cancer that use CRISPR-Cas9, addressing also the current efforts to develop CRISPR-Cas9-based therapies, focusing on proof-of-concept studies. Finally, the review exposes some of the main challenges that this genome-editing tool faces. The key issue remains: does CRISPR-Cas9 have real potential for therapeutic application or will it just remain a wonderful research tool?
Collapse
Affiliation(s)
- Diogo Estêvão
- Molecular Oncology & Viral Pathology Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal Porto, Portugal.,Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal Porto, Portugal
| | - Natália Rios Costa
- Molecular Oncology & Viral Pathology Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal Porto, Portugal
| | - Rui Gil da Costa
- Laboratory for Process Engineering, Environment, Biotechnology & Energy (LEPABE), Faculty of Engineering of the University of Porto (FEUP), 4200-465 Porto, Portugal.,Center for the Research & Technology of Agro-Environmental & Biological Sciences (CITAB), University of Trás-os-Montes & Alto Douro (UTAD), 5001-911 Vila Real, Portugal
| | - Rui Medeiros
- Molecular Oncology & Viral Pathology Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal Porto, Portugal.,Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal Porto, Portugal.,Research Department of the Portuguese League Against Cancer (Liga Portuguesa Contra o Cancro - Núcleo Regional do Norte), 4200-177 Porto, Portugal Porto, Portugal.,Biomedical Research Center (CEBIMED), Faculty of Health Sciences of the Fernando Pessoa University, 4249-004 Porto, Portugal Porto, Portugal
| |
Collapse
|
39
|
Borrego A, Cabrera WHK, Jensen JR, Correa M, Ribeiro OG, Starobinas N, De Franco M, Pettinicchio A, Dragani TA, Ibañez OCM, Manenti G. Germline control of somatic Kras mutations in mouse lung tumors. Mol Carcinog 2018; 57:745-751. [PMID: 29500885 DOI: 10.1002/mc.22796] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/07/2018] [Accepted: 02/28/2018] [Indexed: 01/07/2023]
Abstract
Somatic KRAS mutations are common in human lung adenocarcinomas and are associated with worse prognosis. In mice, Kras is frequently mutated in both spontaneous and experimentally induced lung tumors, although the pattern of mutation varies among strains, suggesting that such mutations are not random events. We tested if the occurrence of Kras mutations is under genetic control in two mouse intercrosses. Codon 61 mutations were prevalent, but the patterns of nucleotide changes differed between the intercrosses. Whole genome analysis with SNPs in (A/J x C57BL/6)F4 mice revealed a significant linkage between a locus on chromosome 19 and 2 particular codon 61 variants (CTA and CGA). In (AIRmax × AIRmin) F2 mice, there was a significant linkage between SNPs located on distal chromosome 6 (around 135 Mbp) and the frequency of codon 61 mutation. These results reveal the presence of two loci, on chromosomes 6 and 19, that modulate Kras mutation frequency in different mouse intercrosses. These findings indicate that somatic mutation frequency and type are not simple random events, but are under genetic control.
Collapse
Affiliation(s)
- Andrea Borrego
- Laboratório de Imunogenética, Instituto Butantan, São Paulo, Brazil
| | - Wafa H K Cabrera
- Laboratório de Imunogenética, Instituto Butantan, São Paulo, Brazil
| | - José R Jensen
- Laboratório de Imunogenética, Instituto Butantan, São Paulo, Brazil
| | - Mara Correa
- Laboratório de Imunogenética, Instituto Butantan, São Paulo, Brazil
| | | | - Nancy Starobinas
- Laboratório de Imunogenética, Instituto Butantan, São Paulo, Brazil
| | | | - Angela Pettinicchio
- Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Tommaso A Dragani
- Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Olga C M Ibañez
- Laboratório de Imunogenética, Instituto Butantan, São Paulo, Brazil
| | - Giacomo Manenti
- Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| |
Collapse
|
40
|
Chen L, Luan S, Xia B, Liu Y, Gao Y, Yu H, Mu Q, Zhang P, Zhang W, Zhang S, Wei G, Yang M, Li K. Integrated analysis of HPV-mediated immune alterations in cervical cancer. Gynecol Oncol 2018; 149:248-255. [PMID: 29572030 DOI: 10.1016/j.ygyno.2018.01.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 01/25/2018] [Accepted: 01/28/2018] [Indexed: 02/01/2023]
Abstract
OBJECTIVE Human papillomavirus (HPV) infection is the primary cause of cervical cancer. HPV-mediated immune alterations are known to play crucial roles in determining viral persistence and host cell transformation. We sought to thoroughly understand HPV-directed immune alterations in cervical cancer by exploring publically available datasets. METHODS 130 HPV positive and 7 HPV negative cervical cancer cases from The Cancer Genome Atlas were compared for differences in gene expression levels and functional enrichment. Analyses for copy number variation (CNV) and genetic mutation were conducted for differentially expressed immune genes. Kaplan-Meier analysis was performed to assess survival and relapse differences across cases with or without alterations of the identified immune signature genes. RESULTS Genes up-regulated in HPV positive cervical cancer were enriched for various gene ontology terms of immune processes (P=1.05E-14~1.00E-05). Integrated analysis of the differentially expressed immune genes identified 9 genes that displayed either CNV, genetic mutation and/or gene expression changes in at least 10% of the cases of HPV positive cervical cancer. Genomic amplification may cause elevated levels of these genes in some HPV positive cases. Finally, patients with alterations in at least one of the nine signature genes overall had earlier relapse compared to those without any alterations. The altered expression of either TFRC or MMP13 may indicate poor survival for a subset of cervical cancer patients (P=1.07E-07). CONCLUSIONS We identified a novel immune gene signature for HPV positive cervical cancer that is potentially associated with early relapse of cervical cancer.
Collapse
Affiliation(s)
- Long Chen
- Department of Gynecology, Qingdao Municipal Hospital, Qingdao 266011, PR China.
| | - Shaohong Luan
- Department of Gynecology, Qingdao Municipal Hospital, Qingdao 266011, PR China
| | - Baoguo Xia
- Department of Gynecology, Qingdao Municipal Hospital, Qingdao 266011, PR China
| | - Yansheng Liu
- Department of Gynecology, Qingdao Municipal Hospital, Qingdao 266011, PR China
| | - Yuan Gao
- Department of Gynecology, Qingdao Municipal Hospital, Qingdao 266011, PR China
| | - Hongyan Yu
- Department of Gynecology, Qingdao Municipal Hospital, Qingdao 266011, PR China
| | - Qingling Mu
- Department of Gynecology, Qingdao Municipal Hospital, Qingdao 266011, PR China
| | - Ping Zhang
- Department of Gynecology, Qingdao Municipal Hospital, Qingdao 266011, PR China
| | - Weina Zhang
- Department of Gynecology, Qingdao Municipal Hospital, Qingdao 266011, PR China
| | - Shengmiao Zhang
- Department of Gynecology, Qingdao Municipal Hospital, Qingdao 266011, PR China
| | - Guopeng Wei
- Gezhi Research Lab, Building T1, No.722 Yizhou Avenue, Chengdu 610000, PR China
| | - Min Yang
- Gezhi Research Lab, Building T1, No.722 Yizhou Avenue, Chengdu 610000, PR China
| | - Ke Li
- Gezhi Research Lab, Building T1, No.722 Yizhou Avenue, Chengdu 610000, PR China
| |
Collapse
|
41
|
Cannataro VL, Gaffney SG, Stender C, Zhao ZM, Philips M, Greenstein AE, Townsend JP. Heterogeneity and mutation in KRAS and associated oncogenes: evaluating the potential for the evolution of resistance to targeting of KRAS G12C. Oncogene 2018; 37:2444-2455. [PMID: 29453361 DOI: 10.1038/s41388-017-0105-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 10/02/2017] [Accepted: 10/03/2017] [Indexed: 12/19/2022]
Abstract
Activating mutations in RAS genes are associated with approximately 20% of all human cancers. New targeted therapies show preclinical promise in inhibiting the KRAS G12C variant. However, concerns exist regarding the effectiveness of such therapies in vivo given the possibilities of existing intratumor heterogeneity or de novo mutation leading to treatment resistance. We performed deep sequencing of 27 KRAS G12-positive lung tumors to determine the prevalence of other oncogenic mutations within KRAS or within commonly mutated downstream genes that could confer resistance at the time of treatment. We also passaged patient-derived xenografts to assess the potential for novel KRAS mutation to arise during subsequent tumor evolution. Furthermore, we estimate the de novo mutation rate in KRAS position 12 and in genes downstream of KRAS. Finally, we present an approach for estimation of the selection intensity for these point mutations that explains their high prevalence in tumors. We find no evidence of heterogeneity that may compromise KRAS G12C targeted therapy within sequenced lung tumors or passaged xenografts. We find that mutations that confer resistance are even less likely to occur downstream of KRAS than to occur within KRAS. Our approach predicts that BRAF V600E would provide the highest fitness advantage for de novo-resistant subclones. Overall, our findings suggest that resistance to targeted therapy of KRAS G12C-positive tumors is unlikely to be present at the time of treatment and, among the de novo mutations likely to confer resistance, mutations in BRAF, a gene with targeted inhibitors presently available, result in subclones with the highest fitness advantage.
Collapse
Affiliation(s)
| | | | - Carly Stender
- Department of Biostatistics, Yale University, New Haven, CT, USA
| | - Zi-Ming Zhao
- Department of Biostatistics, Yale University, New Haven, CT, USA
| | - Mark Philips
- Departments of Medicine, Cell Biology, and Pharmacology, New York University School of Medicine, New York, NY, USA
| | | | - Jeffrey P Townsend
- Department of Biostatistics, Yale University, New Haven, CT, USA. .,Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA. .,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
| |
Collapse
|
42
|
Warkentin MT, Tammemägi MC, Freedman MT, Ragard LR, Hocking WG, Kvale PA, Brenner DR, Hu P, Riley TL, Commins J, Church TR, Berg CD. Factors Associated With Small Aggressive Non-Small Cell Lung Cancers in the National Lung Screening Trial: A Validation Study. JNCI Cancer Spectr 2018; 2:pkx010. [PMID: 31360836 PMCID: PMC6649725 DOI: 10.1093/jncics/pkx010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/17/2017] [Accepted: 12/11/2017] [Indexed: 12/11/2022] Open
Abstract
Background A small proportion of non-small cell lung cancers (NSCLCs) have been observed to spread to distant lymph nodes (N3) or metastasize (M1) or both, while the primary tumor is small (≤3 cm, T1). These small aggressive NSCLCs (SA-NSLSC) are important as they are clinically significant, may identify unique biologic pathways, and warrant aggressive follow-up and treatment. This study identifies factors associated with SA-NSCLC and attempts to validate a previous finding that women with a family history of lung cancer are at particularly elevated risk of SA-NSCLC. Methods This study used a case-case design within the National Cancer Institute's National Lung Screening Trial (NLST) cohort. Case patients and "control" patients were selected based on TNM staging parameters. Case patients (n = 64) had T1 NSCLCs that were N3 or M1 or both, while "control" patients (n = 206) had T2 or T3, N0 to N2, and M0 NSCLCs. Univariate and multivariable logistic regression were used to identify factors associated with SA-NSCLC. Results In bootstrap bias-corrected multivariable logistic regression models, small aggressive adenocarcinomas were associated with a positive history of emphysema (odds ratio [OR] = 5.15, 95% confidence interval [CI] = 1.63 to 23.00) and the interaction of female sex and a positive family history of lung cancer (OR = 6.55, 95% CI = 1.06 to 50.80). Conclusions Emphysema may play a role in early lung cancer progression. Females with a family history of lung cancer are at increased risk of having small aggressive lung adenocarcinomas. These results validate previous findings and encourage research on the role of female hormones interacting with family history and genetic factors in lung carcinogenesis and progression.
Collapse
Affiliation(s)
- Matthew T Warkentin
- Department of Health Sciences, Brock University, St. Catharine's, Ontario, Canada.,Department of Cancer Epidemiology and Prevention Research, CancerControl Alberta, Alberta Health Services, Calgary, Alberta, Canada
| | - Martin C Tammemägi
- Department of Health Sciences, Brock University, St. Catharine's, Ontario, Canada
| | - Matthew T Freedman
- Cancer Prevention and Control, Georgetown Lombardi Comprehensive Cancer Center, Washington, DC
| | | | - William G Hocking
- Department of Clinical Oncology, Marshfield Clinic Health System, Marshfield, WI
| | - Paul A Kvale
- Division of Pulmonary and Critical Care Medicine, Henry Ford Health System, Detroit, MI
| | - Darren R Brenner
- Department of Cancer Epidemiology and Prevention Research, CancerControl Alberta, Alberta Health Services, Calgary, Alberta, Canada.,Departments of Community Health Sciences and Oncology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Ping Hu
- Biometry Research Group, National Cancer Institute, Bethesda, MD
| | | | - John Commins
- Information Management Services, Inc., Rockville, MD
| | - Timothy R Church
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN
| | - Christine D Berg
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| |
Collapse
|
43
|
The 2015 World Health Organisation Classification of Lung Cancer. PRECISION MOLECULAR PATHOLOGY OF LUNG CANCER 2018. [DOI: 10.1007/978-3-319-62941-4_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
44
|
Kim SJ, Kim E, Rim KT. Non-invasive quantification of cell-free DNA mutations in plasma during lung tumor progression in mice. Cancer Biomark 2017; 20:477-485. [PMID: 28946552 DOI: 10.3233/cbm-170303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Testing carcinogenicity caused by chemicals requires a noninvasive tool that can be used before autopsy because autopsy takes a long time. We investigated whether non-small cell lung cancer related gene mutations could be detected in cell-free DNA in plasma by Insight OncoTM next-generation sequencing, which is a fast and sensitive method. Adenoma formation was confirmed in urethane-injected 17-week-old mice. Seven single nucleotide polymorphisms, such as Cdkn2a and Vegfa, were selected. Mutant-enriched Insight OncoTM NGS and normal NGS were performed on genomic DNA. The results demonstrate that Insight OncoTM NGS detected Cdkn2a and Vegfa SNPs at 0.05%. The sensitivity of Insight OncoTM NGS was twice higher than that of normal NGS. In this analysis, the Cdkn2a gene mutation was detected not only in two genomic DNA samples of lung tissue from the 11th week of urethane injection but also in two cell-free DNA samples. In addition, the Vegfa gene mutation was detected not only in three genomic DNA samples of lung tissue of injection but also in one cell-free DNA sample, showing 33% concordance. Our results confirm that Insight OncoTM NGS is a rapid and sensitive detection method that enables lung cancer-associated gene mutations to be detected in cell-free DNA before the end of the carcinogenicity test.
Collapse
Affiliation(s)
- Soo-Jin Kim
- Chemicals Research Bureau, Occupational Safety and Health Research Institute, Korea Occupational Safety and Health Agency, Daejeon 34122, Korea.,Department of Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Korea
| | - Eunhee Kim
- Department of Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Korea
| | - Kyung-Taek Rim
- Chemicals Research Bureau, Occupational Safety and Health Research Institute, Korea Occupational Safety and Health Agency, Daejeon 34122, Korea
| |
Collapse
|
45
|
Naidu S, Shi L, Magee P, Middleton JD, Laganá A, Sahoo S, Leong HS, Galvin M, Frese K, Dive C, Guzzardo V, Fassan M, Garofalo M. PDGFR-modulated miR-23b cluster and miR-125a-5p suppress lung tumorigenesis by targeting multiple components of KRAS and NF-kB pathways. Sci Rep 2017; 7:15441. [PMID: 29133857 PMCID: PMC5684387 DOI: 10.1038/s41598-017-14843-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/17/2017] [Indexed: 02/07/2023] Open
Abstract
In NSCLC alterations in PDGF receptors are markers of worst prognosis and efficient targeting of these receptors is yet to be achieved. In this study, we explored PDGFR-regulated microRNAs demonstrating that miR-23b cluster and miR-125a-5p are downregulated by increased expression of PDGFR-α or PDGFR-β in NSCLC cells. Mechanistically, the expression of these microRNAs is positively regulated by p53 and negatively modulated by NF-kB p65. Forced expression of miR-23b cluster or miR-125a-5p enhanced drug sensitivity and suppressed invasiveness of NSCLC cells by silencing several genes involved in oncogenic KRAS and NF-kB pathways, including SOS1, GRB2, IQGAP1, RALA, RAF-1, IKKβ, AKT2, ERK2 and KRAS itself. Of note, an inverse correlation between miR-23b cluster, miR-125a-5p and respective target genes was also found in vivo in a large dataset of lung adenocarcinoma samples. Furthermore, in vivo delivery of miR-23b cluster or miR-125a-5p significantly repressed tumour growth in a highly aggressive NSCLC circulating tumour cell (CTC) patient derived explant (CDX) mouse model. In conclusion, our finding sheds light on the PDGFR signaling and endorses the possibility to employ miR-23b cluster and miR-125a-5p as therapeutic tools to silence simultaneously a range of redundant pathways and main effectors of tumorigenesis in NSCLC.
Collapse
Affiliation(s)
- Srivatsava Naidu
- Transcriptional Networks in Lung Cancer Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Lei Shi
- Transcriptional Networks in Lung Cancer Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
- Cancer Research UK Lung Cancer Centre of Excellence, at Manchester and University College London, London, UK
| | - Peter Magee
- Transcriptional Networks in Lung Cancer Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Justin D Middleton
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, USA
| | - Alessandro Laganá
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, USA
| | - Sudhakar Sahoo
- Computational Biology Support Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Hui Sun Leong
- Computational Biology Support Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
| | - Melanie Galvin
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
- Cancer Research UK Lung Cancer Centre of Excellence, at Manchester and University College London, London, UK
| | - Kristopher Frese
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
- Cancer Research UK Lung Cancer Centre of Excellence, at Manchester and University College London, London, UK
| | - Caroline Dive
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
- Cancer Research UK Lung Cancer Centre of Excellence, at Manchester and University College London, London, UK
| | - Vincenza Guzzardo
- Department of Medicine, Surgical Pathology Unit, University of Padua, Padua, Italy
| | - Matteo Fassan
- Department of Medicine, Surgical Pathology Unit, University of Padua, Padua, Italy
| | - Michela Garofalo
- Transcriptional Networks in Lung Cancer Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, at Manchester and University College London, London, UK.
| |
Collapse
|
46
|
Targeted next-generation sequencing for analyzing the genetic alterations in atypical adenomatous hyperplasia and adenocarcinoma in situ. J Cancer Res Clin Oncol 2017; 143:2447-2453. [DOI: 10.1007/s00432-017-2500-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 08/10/2017] [Indexed: 01/04/2023]
|
47
|
Cassidy RJ, Zhang X, Patel PR, Shelton JW, Escott CE, Sica GL, Rossi MR, Hill CE, Steuer CE, Pillai RN, Ramalingam SS, Owonikoko TK, Behera M, Force SD, Fernandez FG, Curran WJ, Higgins KA. Next-generation sequencing and clinical outcomes of patients with lung adenocarcinoma treated with stereotactic body radiotherapy. Cancer 2017; 123:3681-3690. [PMID: 28608966 DOI: 10.1002/cncr.30794] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/04/2017] [Accepted: 04/26/2017] [Indexed: 12/25/2022]
Abstract
BACKGROUND Genetic aberrations are well characterized in lung adenocarcinomas (LACs) and clinical outcomes have been influenced by targeted therapies in the advanced setting. Stereotactic body radiotherapy (SBRT) is the standard-of-care therapy for patients with nonoperable, early-stage LAC, but to the authors' knowledge, no information is available regarding the impact of genomic changes in these patients. The current study sought to determine the frequency and clinical impact of genetic aberrations in this population. METHODS Under an Institutional Review Board-approved protocol, the records of 242 consecutive patients with early-stage lung cancers were reviewed; inclusion criteria included LAC histology with an adequate tumor sample for the successful use of next-generation sequencing and fluorescence in situ hybridization testing. Univariate analysis was performed to identify factors associated with clinical outcomes. RESULTS LAC samples from 98 of the 242 patients were reviewed (40.5%), of whom 45 patients (46.0%) had genetic testing. The following mutations were noted: KRAS in 20.0% of samples, BRAF in 2.2% of samples, SMAD family member 4 (SMAD4) in 4.4% of samples, epidermal growth factor receptor (EGFR) in 15.6% of samples, STK1 in 2.2% of samples, tumor protein 53 (TP53) in 15.6% of samples, and phosphatase and tensin homolog (PTEN) in 2.2% of samples. The following gene rearrangements were observed: anaplastic lymphoma kinase (ALK) in 8.9% of samples, RET in 2.2% of samples, and MET amplification in 17.8% of samples. The median total delivered SBRT dose was 50 grays (range, 48-60 grays) over a median of 5 fractions (range, 3-8 fractions). The KRAS mutation was associated with worse local control (odds ratio [OR], 3.64; P<.05). MET amplification was associated with worse regional (OR, 4.64; P<.05) and distant (OR, 3.73; P<.05) disease control. CONCLUSIONS To the authors' knowledge, the current series is the first to quantify genetic mutations and their association with clinical outcomes in patients with early-stage LAC treated with SBRT. KRAS mutations were associated with worse local control and MET amplification was associated with worse regional and distant disease control, findings that need to be validated in a prospective setting. Cancer 2017;123:3681-3690. © 2017 American Cancer Society.
Collapse
Affiliation(s)
- Richard J Cassidy
- Department of Radiation Oncology, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Xinyan Zhang
- Department of Biostatistics and Bioinformatics, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Pretesh R Patel
- Department of Radiation Oncology, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Joseph W Shelton
- Department of Radiation Oncology, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Chase E Escott
- Department of Radiation Oncology, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Gabriel L Sica
- Department of Pathology, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Michael R Rossi
- Department of Radiation Oncology, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Charles E Hill
- Department of Pathology, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Conor E Steuer
- Department of Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Rathi N Pillai
- Department of Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Suresh S Ramalingam
- Department of Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Taofeek K Owonikoko
- Department of Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Madhusmita Behera
- Department of Biostatistics and Bioinformatics, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Seth D Force
- Department of Thoracic Surgery, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Felix G Fernandez
- Department of Thoracic Surgery, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Walter J Curran
- Department of Radiation Oncology, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Kristin A Higgins
- Department of Radiation Oncology, Winship Cancer Institute of Emory University, Atlanta, Georgia
| |
Collapse
|
48
|
Prevalence of NRAS, PTEN and AKT1 gene mutations in the central nervous system metastases of non-small cell lung cancer. Brain Tumor Pathol 2017; 34:36-41. [PMID: 28097440 PMCID: PMC5344951 DOI: 10.1007/s10014-016-0276-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 12/23/2016] [Indexed: 12/12/2022]
Abstract
Somatic mutations in NRAS, PTEN and AKT1 genes are rarely (~1%) reported in primary NSCLC, but their role in carcinogenesis have been proven. Therefore, we assessed the frequency of them in 145 FFPE tissue samples from CNS metastases of NSCLC using the real-time PCR technique. We identified four (two NRAS and single AKT1 and PTEN) mutations in CNS metastases of NSCLC. All mutations were observed in current male smokers (4% out of the male group; 4/100 and 4.25% out of smokers; 4/94). Three mutations have been detected in patients with SqCC (10.3% out of SqCC patients; 3/29), and only one mutation in the NRAS gene—in a patient with adenocarcinoma (1.25% out of AC patients; 1/80). The examined genes were mutually exclusive in terms of molecular background in KRAS; EGFR; DDR2; PIK3CA; HER2 and MEK1 genes that were evaluated in our previous studies. The OS of the patients who harbored NRAS, AKT1 and PTEN mutations was 10.1, 12.1, 7.3 and 4 months, respectively (vs 13.5 months of the studied group). Our results suggest that the presence of NRAS, PTEN and AKT1 gene mutations may have an influence on the occurrence of CNS metastases in patients with SqCC.
Collapse
|
49
|
Mendes R, Carreira B, Baptista PV, Fernandes AR. Non-small cell lung cancer biomarkers and targeted therapy - two faces of the same coin fostered by nanotechnology. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2016. [DOI: 10.1080/23808993.2016.1159914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
50
|
Ross JS, Wang K, Khaira D, Ali SM, Fisher HAG, Mian B, Nazeer T, Elvin JA, Palma N, Yelensky R, Lipson D, Miller VA, Stephens PJ, Subbiah V, Pal SK. Comprehensive genomic profiling of 295 cases of clinically advanced urothelial carcinoma of the urinary bladder reveals a high frequency of clinically relevant genomic alterations. Cancer 2015; 122:702-11. [PMID: 26651075 DOI: 10.1002/cncr.29826] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 08/19/2015] [Accepted: 08/24/2015] [Indexed: 11/10/2022]
Abstract
BACKGROUND In the current study, the authors present a comprehensive genomic profile (CGP)-based study of advanced urothelial carcinoma (UC) designed to detect clinically relevant genomic alterations (CRGAs). METHODS DNA was extracted from 40 µm of formalin-fixed, paraffin-embedded sections from 295 consecutive cases of recurrent/metastatic UC. CGP was performed on hybridization-captured, adaptor ligation-based libraries to a mean coverage depth of 688X for all coding exons of 236 cancer-related genes plus 47 introns from 19 genes frequently rearranged in cancer, using process-matched normal control samples as a reference. CRGAs were defined as GAs linked to drugs on the market or currently under evaluation in mechanism-driven clinical trials. RESULTS All 295 patients assessed were classified with high-grade (International Society of Urological Pathology classification) and advanced stage (stage III/IV American Joint Committee on Cancer) disease, and 294 of 295 patients (99.7%) had at least 1 GA on CGP with a mean of 6.4 GAs per UC (61% substitutions/insertions/deletions, 37% copy number alterations, and 2% fusions). Furthermore, 275 patients (93%) had at least 1 CRGA involving 75 individual genes with a mean of 2.6 CRGAs per UC. The most common CRGAs involved cyclin-dependent kinase inhibitor 2A (CDKN2A) (34%), fibroblast growth factor receptor 3 (FGFR3) (21%), phosphatidylinositol 3-kinase catalytic subunit alpha (PIK3CA) (20%), and ERBB2 (17%). FGFR3 GAs were diverse types and included 10% fusions. ERBB2 GAs were equally divided between amplifications and substitutions. ERBB2 substitutions were predominantly within the extracellular domain and were highly enriched in patients with micropapillary UC (38% of 32 cases vs 5% of 263 nonmicropapillary UC cases; P<.0001). CONCLUSIONS Using a CGP assay capable of detecting all classes of GA simultaneously, an extraordinarily high frequency of CRGA was identified in a large series of patients with advanced UC. Cancer 2016;122:702-711. © 2015 American Cancer Society.
Collapse
Affiliation(s)
- Jeffrey S Ross
- Department of Pathology and Laboratory Medicine, Albany Medical College Albany, New York.,Department of Clinical Development, Foundation Medicine Inc, Cambridge, Massachusetts
| | - Kai Wang
- Department of Clinical Development, Foundation Medicine Inc, Cambridge, Massachusetts
| | - Depinder Khaira
- Department of Clinical Development, Foundation Medicine Inc, Cambridge, Massachusetts
| | - Siraj M Ali
- Department of Clinical Development, Foundation Medicine Inc, Cambridge, Massachusetts
| | - Huge A G Fisher
- Department of Pathology and Laboratory Medicine, Albany Medical College Albany, New York
| | - Badar Mian
- Department of Pathology and Laboratory Medicine, Albany Medical College Albany, New York
| | - Tipu Nazeer
- Department of Pathology and Laboratory Medicine, Albany Medical College Albany, New York
| | - Julia A Elvin
- Department of Clinical Development, Foundation Medicine Inc, Cambridge, Massachusetts
| | - Norma Palma
- Department of Clinical Development, Foundation Medicine Inc, Cambridge, Massachusetts
| | - Roman Yelensky
- Department of Clinical Development, Foundation Medicine Inc, Cambridge, Massachusetts
| | - Doron Lipson
- Department of Clinical Development, Foundation Medicine Inc, Cambridge, Massachusetts
| | - Vincent A Miller
- Department of Clinical Development, Foundation Medicine Inc, Cambridge, Massachusetts
| | - Philip J Stephens
- Department of Clinical Development, Foundation Medicine Inc, Cambridge, Massachusetts
| | - Vivek Subbiah
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sumanta K Pal
- Department of Medical Oncology and Experimental Therapeutics, City of Hope Cancer Center, Duarte, California
| |
Collapse
|