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Visci G, Tolomeo D, Lonoce A, Arshadi A, Bascetta L, Trotta G, van Riel M, Vermeesch JR, Carbone R, Storlazzi CT. A novel method for the isolation of single cells mimicking circulating tumour cells adhered on Smart Bio Surface slides by Laser Capture Microdissection. PLoS One 2024; 19:e0297739. [PMID: 38457477 PMCID: PMC10923433 DOI: 10.1371/journal.pone.0297739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/11/2024] [Indexed: 03/10/2024] Open
Abstract
In recent years, the importance of isolating single cells from blood circulation for several applications, such as non-invasive tumour diagnosis, the monitoring of minimal residual disease, and the analysis of circulating fetal cells for prenatal diagnosis, urged the need to set up innovative methods. For such applications, different methods were developed. All show some weaknesses, especially a limited sensitivity, and specificity. Here we present a new method for isolating a single or a limited number of cells adhered to SBS slides (Tethis S.p.a.) (a glass slide coated with Nanostructured Titanium Dioxide) by Laser Capture Microdissection (LCM) and subsequent Whole Genome Amplification. SBS slides have been shown to have an optimal performance in immobilizing circulating tumour cells (CTCs) from early breast cancer patients. In this work, we spiked cancer cells in blood samples to mimic CTCs. By defining laser parameters to cut intact samples, we were able to isolate genetically intact single cells. We demonstrate that SBS slides are optimally suited for isolating cells using LCM and that this method provides high-quality DNA, ideal for gene-specific assays such as PCR and Sanger sequencing for mutation analysis.
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Affiliation(s)
- Grazia Visci
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - Doron Tolomeo
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - Angelo Lonoce
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - Aram Arshadi
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | | | - Gianluca Trotta
- Institute of Intelligent Industrial Technologies and Systems for Advanced Manufacturing, Consiglio Nazionale delle Ricerche, Bari, Italy
| | | | | | | | - Clelia Tiziana Storlazzi
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
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2
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Gallagher RI, Wulfkuhle J, Wolf DM, Brown-Swigart L, Yau C, O'Grady N, Basu A, Lu R, Campbell MJ, Magbanua MJ, Coppé JP, Asare SM, Sit L, Matthews JB, Perlmutter J, Hylton N, Liu MC, Symmans WF, Rugo HS, Isaacs C, DeMichele AM, Yee D, Pohlmann PR, Hirst GL, Esserman LJ, van 't Veer LJ, Petricoin EF. Protein signaling and drug target activation signatures to guide therapy prioritization: Therapeutic resistance and sensitivity in the I-SPY 2 Trial. Cell Rep Med 2023; 4:101312. [PMID: 38086377 PMCID: PMC10772394 DOI: 10.1016/j.xcrm.2023.101312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 07/03/2023] [Accepted: 11/14/2023] [Indexed: 12/22/2023]
Abstract
Molecular subtyping of breast cancer is based mostly on HR/HER2 and gene expression-based immune, DNA repair deficiency, and luminal signatures. We extend this description via functional protein pathway activation mapping using pre-treatment, quantitative expression data from 139 proteins/phosphoproteins from 736 patients across 8 treatment arms of the I-SPY 2 Trial (ClinicalTrials.gov: NCT01042379). We identify predictive fit-for-purpose, mechanism-of-action-based signatures and individual predictive protein biomarker candidates by evaluating associations with pathologic complete response. Elevated levels of cyclin D1, estrogen receptor alpha, and androgen receptor S650 associate with non-response and are biomarkers for global resistance. We uncover protein/phosphoprotein-based signatures that can be utilized both for molecularly rationalized therapeutic selection and for response prediction. We introduce a dichotomous HER2 activation response predictive signature for stratifying triple-negative breast cancer patients to either HER2 or immune checkpoint therapy response as a model for how protein activation signatures provide a different lens to view the molecular landscape of breast cancer and synergize with transcriptomic-defined signatures.
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Affiliation(s)
- Rosa I Gallagher
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA 20110, USA.
| | - Julia Wulfkuhle
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA 20110, USA.
| | - Denise M Wolf
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Lamorna Brown-Swigart
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Christina Yau
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nicholas O'Grady
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Amrita Basu
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ruixiao Lu
- Quantum Leap Healthcare Collaborative, San Francisco, CA 94118, USA
| | - Michael J Campbell
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mark J Magbanua
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jean-Philippe Coppé
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Smita M Asare
- Quantum Leap Healthcare Collaborative, San Francisco, CA 94118, USA
| | - Laura Sit
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeffrey B Matthews
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Nola Hylton
- Department of Radiology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Minetta C Liu
- Department of Surgery, Mayo Clinic, Rochester, MN 55905, USA
| | - W Fraser Symmans
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hope S Rugo
- Division of Hematology/Oncology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Claudine Isaacs
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20007, USA
| | - Angela M DeMichele
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Douglas Yee
- Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Paula R Pohlmann
- Department of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gillian L Hirst
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Laura J Esserman
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Laura J van 't Veer
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA 20110, USA.
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3
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Abu-Khalaf MM, Alex Hodge K, Hatzis C, Baldelli E, El Gazzah E, Valdes F, Sikov WM, Mita MM, Denduluri N, Murphy R, Zelterman D, Liotta L, Dunetz B, Dunetz R, Petricoin EF, Pierobon M. AKT/mTOR signaling modulates resistance to endocrine therapy and CDK4/6 inhibition in metastatic breast cancers. NPJ Precis Oncol 2023; 7:18. [PMID: 36797347 PMCID: PMC9935518 DOI: 10.1038/s41698-023-00360-5] [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: 11/07/2022] [Accepted: 02/07/2023] [Indexed: 02/18/2023] Open
Abstract
Endocrine therapy (ET) in combination with CDK4/6 inhibition is routinely used as first-line treatment for HR+/HER2- metastatic breast cancer (MBC) patients. However, 30-40% of patients quickly develop disease progression. In this open-label multicenter clinical trial, we utilized a hypothesis-driven protein/phosphoprotein-based approach to identify predictive markers of response to ET plus CDK4/6 inhibition in pre-treatment tissue biopsies. Pathway-centered signaling profiles were generated from microdissected tumor epithelia and surrounding stroma/immune cells using the reverse phase protein microarray. Phosphorylation levels of the CDK4/6 downstream substrates Rb (S780) and FoxM1 (T600) were higher in patients with progressive disease (PD) compared to responders (p = 0.02). Systemic PI3K/AKT/mTOR activation in tumor epithelia and stroma/immune cells was detected in patients with PD. This activation was not explained by underpinning genomic alterations alone. As the number of FDA-approved targeted compounds increases, functional protein-based signaling analyses may become a critical component of response prediction and treatment selection for MBC patients.
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Affiliation(s)
- Maysa M. Abu-Khalaf
- grid.415231.00000 0004 0577 7855Sidney Kimmel Cancer Center at Thomas Jefferson University, Philadelphia, PA USA
| | - K. Alex Hodge
- grid.22448.380000 0004 1936 8032School of Systems Biology, Center for Applied Proteomics and Molecular Medicine, George Mason University, Fairfax, VA USA
| | | | - Elisa Baldelli
- grid.22448.380000 0004 1936 8032School of Systems Biology, Center for Applied Proteomics and Molecular Medicine, George Mason University, Fairfax, VA USA
| | - Emna El Gazzah
- grid.22448.380000 0004 1936 8032School of Systems Biology, Center for Applied Proteomics and Molecular Medicine, George Mason University, Fairfax, VA USA
| | - Frances Valdes
- grid.419791.30000 0000 9902 6374Sylvester Comprehensive Cancer Center (UM SCCC), University of Miami, Miami, FL USA
| | - William M. Sikov
- grid.241223.4Women and Infants Hospital of Rhode Island, Providence, RI USA
| | - Monica M. Mita
- grid.50956.3f0000 0001 2152 9905Cedars-Sinai Medical Center, Los Angeles, CA USA
| | - Neelima Denduluri
- grid.492966.60000 0004 0481 8256Virginia Cancer Specialists, Fairfax, VA USA
| | - Rita Murphy
- grid.415231.00000 0004 0577 7855Sidney Kimmel Cancer Center at Thomas Jefferson University, Philadelphia, PA USA
| | | | - Lance Liotta
- grid.22448.380000 0004 1936 8032School of Systems Biology, Center for Applied Proteomics and Molecular Medicine, George Mason University, Fairfax, VA USA
| | | | - Rick Dunetz
- grid.490989.5Side Out Foundation, Fairfax, VA USA
| | - Emanuel F. Petricoin
- grid.22448.380000 0004 1936 8032School of Systems Biology, Center for Applied Proteomics and Molecular Medicine, George Mason University, Fairfax, VA USA
| | - Mariaelena Pierobon
- School of Systems Biology, Center for Applied Proteomics and Molecular Medicine, George Mason University, Fairfax, VA, USA.
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Baldelli E, Mandarano M, Bellezza G, Petricoin EF, Pierobon M. Analysis of neuroendocrine clones in NSCLCs using an immuno-guided laser-capture microdissection-based approach. CELL REPORTS METHODS 2022; 2:100271. [PMID: 36046628 PMCID: PMC9421534 DOI: 10.1016/j.crmeth.2022.100271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 06/03/2022] [Accepted: 07/21/2022] [Indexed: 11/30/2022]
Abstract
Clonal evolution and lineage plasticity are key contributors to tumor heterogeneity and response to treatment in cancer. However, capturing signal transduction events in coexisting clones remains challenging from a technical perspective. In this study, we developed and tested a signal-transduction-based workflow to isolate and profile coexisting clones within a complex cellular system like non-small cell lung cancers (NSCLCs). Cooccurring clones were isolated under immunohistochemical guidance using laser-capture microdissection, and cell signaling activation portraits were measured using the reverse-phase protein microarray. To increase the translational potential of this work and capture druggable vulnerabilities within different clones, we measured expression/activation of a panel of key drug targets and downstream substrates of FDA-approved or investigational agents. We isolated intermixed clones, including poorly represented ones (<5% of cells), within the tumor microecology and identified molecular characteristics uniquely attributable to cancer cells that undergo lineage plasticity and neuroendocrine transdifferentiation in NSCLCs.
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Affiliation(s)
- Elisa Baldelli
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Martina Mandarano
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
- Department of Medicine and Surgery, Section of Anatomic Pathology and Histology, University of Perugia, Perugia, Italy
| | - Guido Bellezza
- Department of Medicine and Surgery, Section of Anatomic Pathology and Histology, University of Perugia, Perugia, Italy
| | - Emanuel F. Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
- School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
- School of Systems Biology, George Mason University, Manassas, VA, USA
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Liotta LA, Pappalardo PA, Carpino A, Haymond A, Howard M, Espina V, Wulfkuhle J, Petricoin E. Laser Capture Proteomics: spatial tissue molecular profiling from the bench to personalized medicine. Expert Rev Proteomics 2021; 18:845-861. [PMID: 34607525 PMCID: PMC10720974 DOI: 10.1080/14789450.2021.1984886] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/21/2021] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Laser Capture Microdissection (LCM) uses a laser to isolate, or capture, specific cells of interest in a complex heterogeneous tissue section, under direct microscopic visualization. Recently, there has been a surge of publications using LCM for tissue spatial molecular profiling relevant to a wide range of research topics. AREAS COVERED We summarize the many advances in tissue Laser Capture Proteomics (LCP) using mass spectrometry for discovery, and protein arrays for signal pathway network mapping. This review emphasizes: a) transition of LCM phosphoproteomics from the lab to the clinic for individualized cancer therapy, and b) the emerging frontier of LCM single cell molecular analysis combining proteomics with genomic, and transcriptomic analysis. The search strategy was based on the combination of MeSH terms with expert refinement. EXPERT OPINION LCM is complemented by a rich set of instruments, methodology protocols, and analytical A.I. (artificial intelligence) software for basic and translational research. Resolution is advancing to the tissue single cell level. A vision for the future evolution of LCM is presented. Emerging LCM technology is combining digital and AI guided remote imaging with automation, and telepathology, to a achieve multi-omic profiling that was not previously possible.
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Affiliation(s)
- Lance A. Liotta
- Center For Applied Proteomics and Molecular Medicine (CAPMM) School of Systems Biology, College of Sciences, George Mason University, Manassas, VA 20110, USA
| | - Philip A. Pappalardo
- Center For Applied Proteomics and Molecular Medicine (CAPMM) School of Systems Biology, College of Sciences, George Mason University, Manassas, VA 20110, USA
| | - Alan Carpino
- Fluidigm Corporation, South San Francisco, CA, USA
| | - Amanda Haymond
- Center For Applied Proteomics and Molecular Medicine (CAPMM) School of Systems Biology, College of Sciences, George Mason University, Manassas, VA 20110, USA
| | - Marissa Howard
- Center For Applied Proteomics and Molecular Medicine (CAPMM) School of Systems Biology, College of Sciences, George Mason University, Manassas, VA 20110, USA
| | - Virginia Espina
- Center For Applied Proteomics and Molecular Medicine (CAPMM) School of Systems Biology, College of Sciences, George Mason University, Manassas, VA 20110, USA
| | - Julie Wulfkuhle
- Center For Applied Proteomics and Molecular Medicine (CAPMM) School of Systems Biology, College of Sciences, George Mason University, Manassas, VA 20110, USA
| | - Emanuel Petricoin
- Center For Applied Proteomics and Molecular Medicine (CAPMM) School of Systems Biology, College of Sciences, George Mason University, Manassas, VA 20110, USA
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Akcakanat A, Zheng X, Cruz Pico CX, Kim TB, Chen K, Korkut A, Sahin A, Holla V, Tarco E, Singh G, Damodaran S, Mills GB, Gonzalez-Angulo AM, Meric-Bernstam F. Genomic, Transcriptomic, and Proteomic Profiling of Metastatic Breast Cancer. Clin Cancer Res 2021; 27:3243-3252. [PMID: 33782032 PMCID: PMC8172429 DOI: 10.1158/1078-0432.ccr-20-4048] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/10/2020] [Accepted: 03/26/2021] [Indexed: 12/28/2022]
Abstract
PURPOSE Metastatic breast cancer (MBC) is not curable and there is a growing interest in personalized therapy options. Here we report molecular profiling of MBC focusing on molecular evolution in actionable alterations. EXPERIMENTAL DESIGN Sixty-two patients with MBC were included. An analysis of DNA, RNA, and functional proteomics was done, and matched primary and metastatic tumors were compared when feasible. RESULTS Targeted exome sequencing of 41 tumors identified common alterations in TP53 (21; 51%) and PIK3CA (20; 49%), as well as alterations in several emerging biomarkers such as NF1 mutations/deletions (6; 15%), PTEN mutations (4; 10%), and ARID1A mutations/deletions (6; 15%). Among 27 hormone receptor-positive patients, we identified MDM2 amplifications (3; 11%), FGFR1 amplifications (5; 19%), ATM mutations (2; 7%), and ESR1 mutations (4; 15%). In 10 patients with matched primary and metastatic tumors that underwent targeted exome sequencing, discordances in actionable alterations were common, including NF1 loss in 3 patients, loss of PIK3CA mutation in 1 patient, and acquired ESR1 mutations in 3 patients. RNA sequencing in matched samples confirmed loss of NF1 expression with genomic NF1 loss. Among 33 patients with matched primary and metastatic samples that underwent RNA profiling, 14 actionable genes were differentially expressed, including antibody-drug conjugate targets LIV-1 and B7-H3. CONCLUSIONS Molecular profiling in MBC reveals multiple common as well as less frequent but potentially actionable alterations. Genomic and transcriptional profiling demonstrates intertumoral heterogeneity and potential evolution of actionable targets with tumor progression. Further work is needed to optimize testing and integrated analysis for treatment selection.
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Affiliation(s)
- Argun Akcakanat
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xiaofeng Zheng
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christian X Cruz Pico
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Tae-Beom Kim
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anil Korkut
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Aysegul Sahin
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Vijaykumar Holla
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Emily Tarco
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gopal Singh
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Senthil Damodaran
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gordon B Mills
- Department of Cell, Developmental and Cancer Biology, Department of Medicine, Oregon Health and Science University, Portland, Oregon
- Precision Oncology, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Ana Maria Gonzalez-Angulo
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas.
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Magnetic Resonance Features of Lower-grade Gliomas in Prediction of the Reverse Phase Protein A. J Comput Assist Tomogr 2021; 45:300-307. [PMID: 33512852 DOI: 10.1097/rct.0000000000001132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES The Cancer Genome Atlas Research Network identified 4 novel protein expression-defined subgroups in patients with lower-grade gliomas (LGGs). The RPPA3 subtype had high levels of Epidermal Growth Factor Receptor and Human epidermal growth factor receptor-2, further increasing the chances for targeted therapy. In this study, we aimed to explore the relationships between magnetic resonance features and reverse phase protein array (RPPA) subtypes (R1-R4). METHODS Survival estimates for the Cancer Genome Atlas cohort were generated using the Kaplan-Meier method and time-dependent receiver operating characteristic curves. A total of 153 patients with LGG with brain magnetic resonance imaging from The Cancer Imaging Archive were retrospectively analyzed. Least absolute shrinkage and selection operator algorithm was used to reduce the feature dimensions of the RPPA3 subtype. RESULTS A total of 51 (33.3%) RPPA1 subtype, 42 (27.4) RPPA2 subtype, 19 (12.4%) RPPA3 subtype, and 38 (24.8%) RPPA4 subtype were identified. On multivariate logistic regression analysis, subventricular zone involvement [odds ratio (OR), 0.370; P = 0.006; 95% confidence interval (CI), 0.181-0.757) was associated with RPPA1 subtype [area under the curve (AUC), 0.598]. Volume of 60 cm3 or greater (OR, 5.174; P < 0.001; 95% CI, 2.182-12.267) was associated with RPPA2 subtype (AUC, 0.684). Proportion contrast-enhanced tumor greater than 5% (OR, 4.722; P = 0.010; 95% CI, 1.456-15.317), extranodular growth (OR, 5.524; P = 0.010; 95% CI, 1.509-20.215), and L/CS ratio equal to or greater than median (OR, 0.132; P = 0.003; 95% CI, 0.035-0.500) were associated with RPPA3 subtype (AUC, 0.825). Proportion contrast-enhanced tumor greater than 5% (OR, 0.206; P = 0.005; 95% CI, 0.068-0.625) was associated with RPPA4 subtype (AUC, 0.638). For the prediction of RPPA3 subtype, the nomogram showed good discrimination, with an AUC of 0.825 (95% CI, 0.711-0.939) and was well calibrated. The RPPA3 subtype was associated with shortest mean overall survival (RPPA3 subtype vs other: 613 vs 873 days; P < 0.05). The time-dependent receiver operating characteristic curves for the RPPA3 subtype was 0.72 (95% CI, 0.60-0.84) for survival at 1 year. Decision curve analysis indicated that prediction for the RPPA3 model was clinically useful. CONCLUSIONS The RPPA3 subtype is an unfavorable prognostic biomarker for overall survival in patients with LGG. Radiogenomics analysis of magnetic resonance features can predict the RPPA subtype preoperatively and may be of clinical value in tailoring the management strategies in patients with LGG.
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