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Randall J, Hunt AL, Nutcharoen A, Johnston L, Chouraichi S, Wang H, Winer A, Wadlow R, Huynh J, Davis J, Corgiat B, Bateman NW, Deeken JF, Petricoin EF, Conrads TP, Cannon TL. Quantitative proteomic analysis of HER2 protein expression in PDAC tumors. Clin Proteomics 2024; 21:24. [PMID: 38509475 PMCID: PMC10953162 DOI: 10.1186/s12014-024-09476-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
Metastatic pancreatic adenocarcinoma (PDAC) is the third leading cause of cancer-related death in the United States, with a 5-year survival rate of only 11%, necessitating identification of novel treatment paradigms. Tumor tissue specimens from patients with PDAC, breast cancer, and other solid tumor malignancies were collected and tumor cells were enriched using laser microdissection (LMD). Reverse phase protein array (RPPA) analysis was performed on enriched tumor cell lysates to quantify a 32-protein/phosphoprotein biomarker panel comprising known anticancer drug targets and/or cancer-related total and phosphorylated proteins, including HER2Total, HER2Y1248, and HER3Y1289. RPPA analysis revealed significant levels of HER2Total in PDAC patients at abundances comparable to HER2-positive (IHC 3+) and HER2-low (IHC 1+ /2+ , FISH-) breast cancer tissues, for which HER2 screening is routinely performed. These data support a critical unmet need for routine clinical evaluation of HER2 expression in PDAC patients and examination of the utility of HER2-directed antibody-drug conjugates in these patients.
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Affiliation(s)
- Jamie Randall
- Inova Schar Cancer Institute, Inova Health System, 8081 Innovation Park Dr, Fairfax, VA, 22031, USA
| | - Allison L Hunt
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, 3289 Woodburn Rd, Annandale, VA, 22042, USA
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
| | - Aratara Nutcharoen
- Inova Schar Cancer Institute, Inova Health System, 8081 Innovation Park Dr, Fairfax, VA, 22031, USA
- Department of Pathology, Inova Fairfax Hospital, 3300 Gallows Road, Falls Church, VA, 22042, USA
| | - Laura Johnston
- Inova Schar Cancer Institute, Inova Health System, 8081 Innovation Park Dr, Fairfax, VA, 22031, USA
| | - Safae Chouraichi
- Inova Schar Cancer Institute, Inova Health System, 8081 Innovation Park Dr, Fairfax, VA, 22031, USA
| | - Hongkun Wang
- Department of Biostatistics, Bioinformatics, and Biomathematics, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Arthur Winer
- Inova Schar Cancer Institute, Inova Health System, 8081 Innovation Park Dr, Fairfax, VA, 22031, USA
| | - Raymond Wadlow
- Inova Schar Cancer Institute, Inova Health System, 8081 Innovation Park Dr, Fairfax, VA, 22031, USA
| | - Jasmine Huynh
- Inova Schar Cancer Institute, Inova Health System, 8081 Innovation Park Dr, Fairfax, VA, 22031, USA
| | - Justin Davis
- Theralink Technologies, Inc., 15000 W 6th Ave, Golden, CO, 80401, USA
| | - Brian Corgiat
- Theralink Technologies, Inc., 15000 W 6th Ave, Golden, CO, 80401, USA
| | - Nicholas W Bateman
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - John F Deeken
- Inova Schar Cancer Institute, Inova Health System, 8081 Innovation Park Dr, Fairfax, VA, 22031, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, 20110, USA
| | - Thomas P Conrads
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, 3289 Woodburn Rd, Annandale, VA, 22042, USA
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
| | - Timothy L Cannon
- Inova Schar Cancer Institute, Inova Health System, 8081 Innovation Park Dr, Fairfax, VA, 22031, USA.
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2
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Albain KS, Yau C, Petricoin EF, Wolf DM, Lang JE, Chien AJ, Haddad T, Forero-Torres A, Wallace AM, Kaplan H, Pusztai L, Euhus D, Nanda R, Elias AD, Clark AS, Godellas C, Boughey JC, Isaacs C, Tripathy D, Lu J, Yung RL, Gallagher RI, Wulfkuhle JD, Brown-Swigart L, Krings G, Chen YY, Potter DA, Stringer-Reasor E, Blair S, Asare SM, Wilson A, Hirst GL, Singhrao R, Buxton M, Clennell JL, Sanil A, Berry S, Asare AL, Matthews JB, DeMichele AM, Hylton NM, Melisko M, Perlmutter J, Rugo HS, Symmans WF, van’t Veer LJ, Yee D, Berry DA, Esserman LJ. Neoadjuvant Trebananib plus Paclitaxel-based Chemotherapy for Stage II/III Breast Cancer in the Adaptively Randomized I-SPY2 Trial-Efficacy and Biomarker Discovery. Clin Cancer Res 2024; 30:729-740. [PMID: 38109213 PMCID: PMC10956403 DOI: 10.1158/1078-0432.ccr-22-2256] [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: 10/28/2022] [Revised: 10/11/2023] [Accepted: 12/13/2023] [Indexed: 12/20/2023]
Abstract
PURPOSE The neutralizing peptibody trebananib prevents angiopoietin-1 and angiopoietin-2 from binding with Tie2 receptors, inhibiting angiogenesis and proliferation. Trebananib was combined with paclitaxel±trastuzumab in the I-SPY2 breast cancer trial. PATIENTS AND METHODS I-SPY2, a phase II neoadjuvant trial, adaptively randomizes patients with high-risk, early-stage breast cancer to one of several experimental therapies or control based on receptor subtypes as defined by hormone receptor (HR) and HER2 status and MammaPrint risk (MP1, MP2). The primary endpoint is pathologic complete response (pCR). A therapy "graduates" if/when it achieves 85% Bayesian probability of success in a phase III trial within a given subtype. Patients received weekly paclitaxel (plus trastuzumab if HER2-positive) without (control) or with weekly intravenous trebananib, followed by doxorubicin/cyclophosphamide and surgery. Pathway-specific biomarkers were assessed for response prediction. RESULTS There were 134 participants randomized to trebananib and 133 to control. Although trebananib did not graduate in any signature [phase III probabilities: Hazard ratio (HR)-negative (78%), HR-negative/HER2-positive (74%), HR-negative/HER2-negative (77%), and MP2 (79%)], it demonstrated high probability of superior pCR rates over control (92%-99%) among these subtypes. Trebananib improved 3-year event-free survival (HR 0.67), with no significant increase in adverse events. Activation levels of the Tie2 receptor and downstream signaling partners predicted trebananib response in HER2-positive disease; high expression of a CD8 T-cell gene signature predicted response in HR-negative/HER2-negative disease. CONCLUSIONS The angiopoietin (Ang)/Tie2 axis inhibitor trebananib combined with standard neoadjuvant therapy increased estimated pCR rates across HR-negative and MP2 subtypes, with probabilities of superiority >90%. Further study of Ang/Tie2 receptor axis inhibitors in validated, biomarker-predicted sensitive subtypes is warranted.
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Affiliation(s)
- Kathy S. Albain
- Loyola University Chicago Stritch School of Medicine, Chicago, IL
| | - Christina Yau
- University of California San Francisco, San Francisco, CA
| | | | - Denise M. Wolf
- University of California San Francisco, San Francisco, CA
| | | | - A. Jo Chien
- University of California San Francisco, San Francisco, CA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Debu Tripathy
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Janice Lu
- University of Southern California, Los Angeles, CA
| | | | | | | | | | - Gregor Krings
- University of California San Francisco, San Francisco, CA
| | - Yunn Yi Chen
- University of California San Francisco, San Francisco, CA
| | | | | | - Sarah Blair
- University of California San Diego, La Jolla, CA
| | - Smita M. Asare
- Quantum Leap Healthcare Collaborative, San Francisco, CA
| | - Amy Wilson
- Quantum Leap Healthcare Collaborative, San Francisco, CA
| | | | - Ruby Singhrao
- University of California San Francisco, San Francisco, CA
| | | | | | | | | | - Adam L. Asare
- Quantum Leap Healthcare Collaborative, San Francisco, CA
| | | | | | - Nola M. Hylton
- University of California San Francisco, San Francisco, CA
| | | | | | - Hope S. Rugo
- University of California San Francisco, San Francisco, CA
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3
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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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4
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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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5
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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: 2] [Impact Index Per Article: 1.0] [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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6
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Shi Z, Wulfkuhle J, Nowicka M, Gallagher RI, Saura C, Nuciforo PG, Calvo I, Andersen J, Passos-Coelho JL, Gil-Gil MJ, Bermejo B, Pratt DA, Ciruelos EM, Villagrasa P, Wongchenko MJ, Petricoin EF, Oliveira M, Isakoff SJ. Functional Mapping of AKT Signaling and Biomarkers of Response from the FAIRLANE Trial of Neoadjuvant Ipatasertib plus Paclitaxel for Triple-Negative Breast Cancer. Clin Cancer Res 2022; 28:993-1003. [PMID: 34907082 PMCID: PMC9377742 DOI: 10.1158/1078-0432.ccr-21-2498] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/27/2021] [Accepted: 12/09/2021] [Indexed: 01/07/2023]
Abstract
PURPOSE Despite extensive genomic and transcriptomic profiling, it remains unknown how signaling pathways are differentially activated and how tumors are differentially sensitized to certain perturbations. Here, we aim to characterize AKT signaling activity and its association with other genomic or IHC-based PI3K/AKT pathway biomarkers as well as the clinical activity of ipatasertib (AKT inhibitor) in the FAIRLANE trial. EXPERIMENTAL DESIGN In FAIRLANE, 151 patients with early triple-negative breast cancer (TNBC) were randomized 1:1 to receive paclitaxel with ipatasertib or placebo for 12 weeks prior to surgery. Adding ipatasertib did not increase pathologic complete response rate and numerically improved overall response rate by MRI. We used reverse-phase protein microarrays (RPPA) to examine the total level and/or phosphorylation states of over 100 proteins in various signaling or cell processes including PI3K/AKT and mTOR signaling. One hundred and twenty-five baseline and 127 on-treatment samples were evaluable by RPPA, with 110 paired samples at both time points. RESULTS Tumors with genomic/protein alterations in PIK3CA/AKT1/PTEN were associated with higher levels of AKT phosphorylation. In addition, phosphorylated AKT (pAKT) levels exhibited a significant association with enriched clinical benefit of ipatasertib, and identified patients who received benefit in the absence of PIK3CA/AKT1/PTEN alterations. Ipatasertib treatment led to a downregulation of AKT/mTORC1 signaling, which was more pronounced among the tumors with PIK3CA/AKT1/PTEN alterations or among the responders to the treatment. CONCLUSIONS We showed that the high baseline pAKT levels are associated with the alterations of PI3K/AKT pathway components and enriched benefit of ipatasertib in TNBC.
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Affiliation(s)
- Zhen Shi
- Department of Oncology Biomarker, Genentech Inc., South San Francisco, California
| | - Julia Wulfkuhle
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia
| | | | - Rosa I. Gallagher
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia
| | - Cristina Saura
- Medical Oncology Department, Vall d’Hebron University Hospital, Barcelona, Spain
- Breast Cancer Group, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
- SOLTI Breast Cancer Research Group, Barcelona, Spain
| | - Paolo G. Nuciforo
- Molecular Oncology Group, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Isabel Calvo
- Breast Cancer Unit, Centro Integral Oncologico Clara Campal (CIOCC), Madrid, Spain
| | - Jay Andersen
- Medical Oncology/Hematology, Compass Oncology, Tigard, Oregon
| | | | - Miguel J. Gil-Gil
- SOLTI Breast Cancer Research Group, Barcelona, Spain
- Medical Oncology Service, Institut Català d’Oncologia, L’Hospitalet, Barcelona, Spain
- Institut d'Investigació Biomédica de Bellvitge (IDIBELL), Barcelona, Spain
| | - Begoña Bermejo
- Hospital Clinico Universitario de Valencia, Valencia, Spain
| | - Debra A. Pratt
- Texas Oncology Cancer Center, US Oncology, Austin, Texas
| | - Eva M. Ciruelos
- SOLTI Breast Cancer Research Group, Barcelona, Spain
- Medical Oncology Department, University Hospital 12 de Octubre, Madrid, Spain
| | | | | | - Emanuel F. Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia
| | - Mafalda Oliveira
- Medical Oncology Department, Vall d’Hebron University Hospital, Barcelona, Spain
- Breast Cancer Group, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
- SOLTI Breast Cancer Research Group, Barcelona, Spain
| | - Steven J. Isakoff
- Division of Hematology/Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
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7
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Diehl JN, Klomp JE, Snare KR, Hibshman PS, Blake DR, Kaiser ZD, Gilbert TSK, Baldelli E, Pierobon M, Papke B, Yang R, Hodge RG, Rashid NU, Petricoin EF, Herring LE, Graves LM, Cox AD, Der CJ. The KRAS-regulated kinome identifies WEE1 and ERK coinhibition as a potential therapeutic strategy in KRAS-mutant pancreatic cancer. J Biol Chem 2021; 297:101335. [PMID: 34688654 PMCID: PMC8591367 DOI: 10.1016/j.jbc.2021.101335] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 09/24/2021] [Accepted: 10/19/2021] [Indexed: 02/07/2023] Open
Abstract
Oncogenic KRAS drives cancer growth by activating diverse signaling networks, not all of which have been fully delineated. We set out to establish a system-wide profile of the KRAS-regulated kinase signaling network (kinome) in KRAS-mutant pancreatic ductal adenocarcinoma (PDAC). We knocked down KRAS expression in a panel of six cell lines and then applied multiplexed inhibitor bead/MS to monitor changes in kinase activity and/or expression. We hypothesized that depletion of KRAS would result in downregulation of kinases required for KRAS-mediated transformation and in upregulation of other kinases that could potentially compensate for the deleterious consequences of the loss of KRAS. We identified 15 upregulated and 13 downregulated kinases in common across the panel of cell lines. In agreement with our hypothesis, all 15 of the upregulated kinases have established roles as cancer drivers (e.g., SRC, TGF-β1, ILK), and pharmacological inhibition of one of these upregulated kinases, DDR1, suppressed PDAC growth. Interestingly, 11 of the 13 downregulated kinases have established driver roles in cell cycle progression, particularly in mitosis (e.g., WEE1, Aurora A, PLK1). Consistent with a crucial role for the downregulated kinases in promoting KRAS-driven proliferation, we found that pharmacological inhibition of WEE1 also suppressed PDAC growth. The unexpected paradoxical activation of ERK upon WEE1 inhibition led us to inhibit both WEE1 and ERK concurrently, which caused further potent growth suppression and enhanced apoptotic death compared with WEE1 inhibition alone. We conclude that system-wide delineation of the KRAS-regulated kinome can identify potential therapeutic targets for KRAS-mutant pancreatic cancer.
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Affiliation(s)
- J Nathaniel Diehl
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jennifer E Klomp
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kayla R Snare
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Priya S Hibshman
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Cell Biology and Physiology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Devon R Blake
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Zane D Kaiser
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Thomas S K Gilbert
- Cell Biology and Physiology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; UNC Michael Hooker Proteomics Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Elisa Baldelli
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - Björn Papke
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Runying Yang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Richard G Hodge
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Naim U Rashid
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - Laura E Herring
- Cell Biology and Physiology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; UNC Michael Hooker Proteomics Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Lee M Graves
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Cell Biology and Physiology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; UNC Michael Hooker Proteomics Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Adrienne D Cox
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Cell Biology and Physiology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Channing J Der
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Cell Biology and Physiology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
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8
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Baldelli E, Hodge KA, Bellezza G, Shah NJ, Gambara G, Sidoni A, Mandarano M, Ruhunusiri C, Dunetz B, Abu-Khalaf M, Wulfkuhle J, Gallagher RI, Liotta L, de Bono J, Mehra N, Riisnaes R, Ravaggi A, Odicino F, Sereni MI, Blackburn M, Zupa A, Improta G, Demsko P, Crino' L, Ludovini V, Giaccone G, Petricoin EF, Pierobon M. PD-L1 quantification across tumor types using the reverse phase protein microarray: implications for precision medicine. J Immunother Cancer 2021; 9:e002179. [PMID: 34620701 PMCID: PMC8499669 DOI: 10.1136/jitc-2020-002179] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Anti-programmed cell death protein 1 and programmed cell death ligand 1 (PD-L1) agents are broadly used in first-line and second-line treatment across different tumor types. While immunohistochemistry-based assays are routinely used to assess PD-L1 expression, their clinical utility remains controversial due to the partial predictive value and lack of standardized cut-offs across antibody clones. Using a high throughput immunoassay, the reverse phase protein microarray (RPPA), coupled with a fluorescence-based detection system, this study compared the performance of six anti-PD-L1 antibody clones on 666 tumor samples. METHODS PD-L1 expression was measured using five antibody clones (22C3, 28-8, CAL10, E1L3N and SP142) and the therapeutic antibody atezolizumab on 222 lung, 71 ovarian, 52 prostate and 267 breast cancers, and 54 metastatic lesions. To capture clinically relevant variables, our cohort included frozen and formalin-fixed paraffin-embedded samples, surgical specimens and core needle biopsies. Pure tumor epithelia were isolated using laser capture microdissection from 602 samples. Correlation coefficients were calculated to assess concordance between antibody clones. For two independent cohorts of patients with lung cancer treated with nivolumab, RPPA-based PD-L1 measurements were examined along with response to treatment. RESULTS Median-center PD-L1 dynamic ranged from 0.01 to 39.37 across antibody clones. Correlation coefficients between the six antibody clones were heterogeneous (range: -0.48 to 0.95) and below 0.50 in 61% of the comparisons. In nivolumab-treated patients, RPPA-based measurement identified a subgroup of tumors, where low PD-L1 expression equated to lack of response. CONCLUSIONS Continuous RPPA-based measurements capture a broad dynamic range of PD-L1 expression in human specimens and heterogeneous concordance levels between antibody clones. This high throughput immunoassay can potentially identify subgroups of tumors in which low expression of PD-L1 equates to lack of response to treatment.
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Affiliation(s)
- Elisa Baldelli
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - K Alex Hodge
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - Guido Bellezza
- Department of Experimental Medicine, Section of Anatomic Pathology and Histology, University of Perugia, Perugia, Italy
| | - Neil J Shah
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
| | - Guido Gambara
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - Angelo Sidoni
- Department of Experimental Medicine, Section of Anatomic Pathology and Histology, University of Perugia, Perugia, Italy
| | - Martina Mandarano
- Department of Experimental Medicine, Section of Anatomic Pathology and Histology, University of Perugia, Perugia, Italy
| | - Chamodya Ruhunusiri
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
- School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | | | - Maysa Abu-Khalaf
- Department of Medical Oncology, Sidney Kimmel Cancer Center at Jefferson Health, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Julia Wulfkuhle
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - Rosa I Gallagher
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - Lance Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | | | - Niven Mehra
- The Institute of Cancer Research, London, UK
| | | | - Antonella Ravaggi
- Angelo Nocivelli Institute of Molecular Medicine, Division of Gynecologic Oncology, University of Brescia and ASST Spedali Civili di Brescia, Brescia, Italy
| | - Franco Odicino
- Angelo Nocivelli Institute of Molecular Medicine, Division of Gynecologic Oncology, University of Brescia and ASST Spedali Civili di Brescia, Brescia, Italy
| | - Maria Isabella Sereni
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
- Angelo Nocivelli Institute of Molecular Medicine, Division of Gynecologic Oncology, University of Brescia and ASST Spedali Civili di Brescia, Brescia, Italy
| | - Matthew Blackburn
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
| | - Angela Zupa
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
- Unita' Operativa di Anatomia Patologica, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) CROB, Rionero In Vulture, Italy
| | - Giuseppina Improta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
- Unita' Operativa di Anatomia Patologica, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) CROB, Rionero In Vulture, Italy
| | - Perry Demsko
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - Lucio Crino'
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Vienna Ludovini
- Division of Medical Oncology, S. Maria della Misericordia Hospital, Perugia, Italy
| | - Giuseppe Giaccone
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
- School of Systems Biology, George Mason University, Manassas, Virginia, USA
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9
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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: 14] [Impact Index Per Article: 4.7] [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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10
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Mechanism of action biomarkers predicting response to AKT inhibition in the I-SPY 2 breast cancer trial. NPJ Breast Cancer 2020; 6:48. [PMID: 33083527 PMCID: PMC7532145 DOI: 10.1038/s41523-020-00189-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 07/22/2020] [Indexed: 12/12/2022] Open
Abstract
The AKT inhibitor MK2206 (M) was evaluated in I-SPY 2 and graduated in
the HER2+, HR−, and HR− HER2+ signatures. We hypothesized that AKT signaling axis
proteins/genes may specifically predict response to M and tested 26 phospho-proteins
and 10 genes involved in AKT-mTOR-HER signaling; in addition, we tested 9 genes from
a previous study in the metastatic setting. One hundred and fifty patients had gene
expression data from pretreatment biopsies available for analysis (M: 94, control:
56) and 138 had protein data (M: 87, control: 51). Logistic modeling was used to
assess biomarker performance in pre-specified analysis. In general, phospho-protein
biomarkers of activity in the AKT-mTOR-HER pathway appeared more predictive of
response to M than gene expression or total protein biomarkers in the same pathway;
however, the nature of the predictive biomarkers differed in the HER2+ and TN
groups. In the HER2+ subset, patients achieving a pCR in M had higher levels of
multiple AKT kinase substrate phospho-proteins (e.g., pmTOR, pTSC2). In contrast, in
the TN subset responding patients had lower levels of AKT pathway phospho-proteins,
such as pAKT, pmTOR, and pTSC2. Pathway mutations did not appear to account for
these associations. Additional exploratory whole-transcriptome analysis revealed
immune signaling as strongly associated with response to M in the HER2+ subset.
While our sample size is small, these results suggest that the measurement of
particular AKT kinase substrate phospho-proteins could be predictive of MK2206
efficacy in both HER2+ and TN tumors and that immune signaling may play a role in
response in HER2+ patients.
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11
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Jafari M, Wang Y, Amiryousefi A, Tang J. Unsupervised Learning and Multipartite Network Models: A Promising Approach for Understanding Traditional Medicine. Front Pharmacol 2020; 11:1319. [PMID: 32982738 PMCID: PMC7479204 DOI: 10.3389/fphar.2020.01319] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/07/2020] [Indexed: 12/11/2022] Open
Abstract
The ultimate goal of precision medicine is to determine right treatment for right patients based on precise diagnosis. To achieve this goal, correct stratification of patients using molecular features and clinical phenotypes is crucial. During the long history of medical science, our understanding on disease classification has been improved greatly by chemistry and molecular biology. Nowadays, we gain access to large scale patient-derived data by high-throughput technologies, generating a greater need for data science including unsupervised learning and network modeling. Unsupervised learning methods such as clustering could be a better solution to stratify patients when there is a lack of predefined classifiers. In network modularity analysis, clustering methods can be also applied to elucidate the complex structure of biological and disease networks at the systems level. In this review, we went over the main points of clustering analysis and network modeling, particularly in the context of Traditional Chinese medicine (TCM). We showed that this approach can provide novel insights on the rationale of classification for TCM herbs. In a case study, using a modularity analysis of multipartite networks, we illustrated that the TCM classifications are associated with the chemical properties of the herb ingredients. We concluded that multipartite network modeling may become a suitable data integration tool for understanding the mechanisms of actions of traditional medicine.
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Affiliation(s)
- Mohieddin Jafari
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Yinyin Wang
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ali Amiryousefi
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jing Tang
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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12
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Hunt AL, Pierobon M, Baldelli E, Oliver J, Mitchell D, Gist G, Bateman NW, Larry Maxwell G, Petricoin EF, Conrads TP. The impact of ultraviolet- and infrared-based laser microdissection technology on phosphoprotein detection in the laser microdissection-reverse phase protein array workflow. Clin Proteomics 2020; 17:9. [PMID: 32165870 PMCID: PMC7061469 DOI: 10.1186/s12014-020-09272-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 02/20/2020] [Indexed: 12/13/2022] Open
Abstract
Reversible protein phosphorylation represents a key mechanism by which signals are transduced in eukaryotic cells. Dysregulated phosphorylation is also a hallmark of carcinogenesis and represents key drug targets in the precision medicine space. Thus, methods that preserve phosphoprotein integrity in the context of clinical tissue analyses are crucially important in cancer research. Here we investigated the impact of UV laser microdissection (UV LMD) and IR laser capture microdissection (IR LCM) on phosphoprotein abundance of key cancer signaling protein targets assessed by reverse-phase protein microarray (RPPA). Tumor epithelial cells from consecutive thin sections obtained from four high-grade serous ovarian cancers were harvested using either UV LMD or IR LCM methods. Phosphoprotein abundances for ten phosphoproteins that represent important drug targets were assessed by RPPA and revealed no significant differences in phosphoprotein integrity from those obtained using higher-energy UV versus the lower-energy IR laser methods.
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Affiliation(s)
- Allison L. Hunt
- Women’s Service Line, Inova Health System, 3300 Gallows Rd., Falls Church, VA 22042 USA
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889 USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA USA
| | - Elisa Baldelli
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA USA
| | - Julie Oliver
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889 USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 720A Rockledge Drive, Suite 100, Bethesda, MD 20817 USA
| | - Dave Mitchell
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889 USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 720A Rockledge Drive, Suite 100, Bethesda, MD 20817 USA
| | - Glenn Gist
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889 USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 720A Rockledge Drive, Suite 100, Bethesda, MD 20817 USA
| | - Nicholas W. Bateman
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889 USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 720A Rockledge Drive, Suite 100, Bethesda, MD 20817 USA
| | - G. Larry Maxwell
- Women’s Service Line, Inova Health System, 3300 Gallows Rd., Falls Church, VA 22042 USA
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889 USA
| | - Emanuel F. Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA USA
| | - Thomas P. Conrads
- Women’s Service Line, Inova Health System, 3300 Gallows Rd., Falls Church, VA 22042 USA
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889 USA
- 3289 Woodburn Rd, Suite 375, Annandale, VA 22003 USA
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13
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Pierobon M, Wulfkuhle J, Liotta LA, Petricoin Iii EF. Utilization of Proteomic Technologies for Precision Oncology Applications. Cancer Treat Res 2019; 178:171-187. [PMID: 31209845 DOI: 10.1007/978-3-030-16391-4_6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genomic analysis of tumor specimens has revealed that cancer is fundamentally a proteomic disease at the functional level: driven by genomically defined derangements, but selected for in the proteins that are encoded and the aberrant activation of signaling and biochemical networks. This activation is measured by posttranslational modifications such as phosphorylation and other modifications that modulate cellular signaling, and these events cannot be effectively measured by genomic analysis alone. Moreover, these signaling networks by and large represent the targets for many FDA-approved and experimental molecularly targeted therapeutics. Consequently, it is important that we consider new classification schemas for oncology based not on tumor site of origin or histology under the microscope but on the functional protein signaling architecture. There are numerous proteomic technologies that could be discussed from a purely technological standpoint, but this chapter will concentrate on an overview of the main proteomic technologies available for conducting protein pathway activation analysis of clinical specimens such as multiplex immunoassays, phospho-specific flow cytometry, reverse phase protein microarrays, quantitative immunohistochemistry, and mass spectrometry. This chapter will focus on the application of these technologies to cancer-based clinical studies evaluating prognostic/predictive markers or for stratifying patients to personalized treatments.
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Affiliation(s)
- Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 20110, Manassas, VA, USA
| | - Julie Wulfkuhle
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 20110, Manassas, VA, USA
| | - Lance A Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 20110, Manassas, VA, USA
| | - Emanuel F Petricoin Iii
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 20110, Manassas, VA, USA.
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14
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RPPA: Origins, Transition to a Validated Clinical Research Tool, and Next Generations of the Technology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1188:1-19. [PMID: 31820380 DOI: 10.1007/978-981-32-9755-5_1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
RPPA technology has graduated from a research tool to an essential component of clinical drug discovery research and personalized medicine. Next generations of RPPA technology will be a single clinical instrument that integrates all the steps of the workflow.
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15
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Gaffney EF, Riegman PH, Grizzle WE, Watson PH. Factors that drive the increasing use of FFPE tissue in basic and translational cancer research. Biotech Histochem 2018; 93:373-386. [PMID: 30113239 DOI: 10.1080/10520295.2018.1446101] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The decision to use 10% neutral buffered formalin fixed, paraffin embedded (FFPE) archival pathology material may be dictated by the cancer research question or analytical technique, or may be governed by national ethical, legal and social implications (ELSI), biobank, and sample availability and access policy. Biobanked samples of common tumors are likely to be available, but not all samples will be annotated with treatment and outcomes data and this may limit their application. Tumors that are rare or very small exist mostly in FFPE pathology archives. Pathology departments worldwide contain millions of FFPE archival samples, but there are challenges to availability. Pathology departments lack resources for retrieving materials for research or for having pathologists select precise areas in paraffin blocks, a critical quality control step. When samples must be sourced from several pathology departments, different fixation and tissue processing approaches create variability in quality. Researchers must decide what sample quality and quality tolerance fit their specific purpose and whether sample enrichment is required. Recent publications report variable success with techniques modified to examine all common species of molecular targets in FFPE samples. Rigorous quality management may be particularly important in sample preparation for next generation sequencing and for optimizing the quality of extracted proteins for proteomics studies. Unpredictable failures, including unpublished ones, likely are related to pre-analytical factors, unstable molecular targets, biological and clinical sampling factors associated with specific tissue types or suboptimal quality management of pathology archives. Reproducible results depend on adherence to pre-analytical phase standards for molecular in vitro diagnostic analyses for DNA, RNA and in particular, extracted proteins. With continuing adaptations of techniques for application to FFPE, the potential to acquire much larger numbers of FFPE samples and the greater convenience of using FFPE in assays for precision medicine, the choice of material in the future will become increasingly biased toward FFPE samples from pathology archives. Recognition that FFPE samples may harbor greater variation in quality than frozen samples for several reasons, including variations in fixation and tissue processing, requires that FFPE results be validated provided a cohort of frozen tissue samples is available.
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Affiliation(s)
- E F Gaffney
- a Biobank Ireland Trust , Malahide , Co Dublin , Ireland
| | - P H Riegman
- b Erasmus Medical Centre , Department of Pathology , Rotterdam , The Netherlands
| | - W E Grizzle
- c Department of Pathology , University of Alabama at Birmingham (UAB) , Birmingham , Alabama , USA
| | - P H Watson
- d BC Cancer Agency , Vancouver Island Center , Victoria , BC , Canada
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16
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Yamazaki M, Yabuki N, Suzuki Y, Ito M, Ikeda A, Natori O, Suzuki M, Kato A. PAXgene-fixed paraffin-embedded sample is applicable to laser capture microdissection with well-balanced RNA quality and tissue morphology. J Toxicol Pathol 2018; 31:213-220. [PMID: 30093792 PMCID: PMC6077159 DOI: 10.1293/tox.2017-0049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 03/13/2018] [Indexed: 12/21/2022] Open
Abstract
Assessing how gene expression analysis by RNA sequencing (RNA-Seq) correlates to a unique morphology is increasingly necessary, and laser capture microdissection (LCM) is a critical research tool for discovering the genes responsible in a region of interest (ROI). Because RNA-Seq requires high-quality RNA, a sample preparation procedure that can preserve morphology and give the required quality of RNA is essential. A PAXgene®-fixed paraffin-embedded (XFPE) block can satisfy the need for high-quality RNA, but there are few reports on adapting the method for LCM, such as how small an ROI is analyzable by RNA-Seq. In this study, we confirmed the morphology and preservation of RNA in XFPE and then assessed the relationship between the size of pieces cut by LCM and their RNA quality. In XFPE, the morphology was similar to that in alcohol-based fixed samples, the quality of the RNA extracted from a whole sample was excellent, that is equivalent to that of a fresh frozen sample, and the quality was maintained over one year later. Three sizes of pieces—large (25,000 µm2), medium (5,000 µm2), and small (1,000 µm2)—were cut by LCM so that the total areas of the sections cut per size were the same. RNA quality was found to be best preserved when tissue was cut into pieces of over 5,000 µm2. In summary, XFPE exhibits good morphology and excellent preservation of RNA quality. Furthermore, it can be a good tool when used with LCM and RNA-Seq, giving well-balanced RNA quality and tissue morphology in the ROI.
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Affiliation(s)
- Masaki Yamazaki
- Research Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba-shi, Shizuoka 412-8513, Japan
| | - Nami Yabuki
- Research Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba-shi, Shizuoka 412-8513, Japan.,Forerunner Pharma Research Co., Ltd., Yokohama Bio Industry Center, 1-6 Suehiro-cho, Tsurumi-ku, Yokohama-shi, Kanagawa 230-0045, Japan
| | - Yasunori Suzuki
- Forerunner Pharma Research Co., Ltd., Yokohama Bio Industry Center, 1-6 Suehiro-cho, Tsurumi-ku, Yokohama-shi, Kanagawa 230-0045, Japan
| | - Mayumi Ito
- Forerunner Pharma Research Co., Ltd., Yokohama Bio Industry Center, 1-6 Suehiro-cho, Tsurumi-ku, Yokohama-shi, Kanagawa 230-0045, Japan
| | - Asuka Ikeda
- Chugai Research Institute for Medical Science, Inc., 1-135, Komakado, Gotemba-shi, Shizuoka 412-8513, Japan
| | - Osamu Natori
- Forerunner Pharma Research Co., Ltd., Yokohama Bio Industry Center, 1-6 Suehiro-cho, Tsurumi-ku, Yokohama-shi, Kanagawa 230-0045, Japan
| | - Masami Suzuki
- Research Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba-shi, Shizuoka 412-8513, Japan.,Forerunner Pharma Research Co., Ltd., Yokohama Bio Industry Center, 1-6 Suehiro-cho, Tsurumi-ku, Yokohama-shi, Kanagawa 230-0045, Japan
| | - Atsuhiko Kato
- Research Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba-shi, Shizuoka 412-8513, Japan
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Parasido EM, Silvestri A, Canzonieri V, Belluco C, Diodoro MG, Milione M, Melotti F, De Maria R, Liotta L, Petricoin EF, Pierobon M. Protein drug target activation homogeneity in the face of intra-tumor heterogeneity: implications for precision medicine. Oncotarget 2018; 8:48534-48544. [PMID: 28159918 PMCID: PMC5564706 DOI: 10.18632/oncotarget.14019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 12/09/2016] [Indexed: 12/17/2022] Open
Abstract
Introduction: Recent studies indicated tumors may be comprised of heterogeneous molecular subtypes and incongruent molecular portraits may emerge if different areas of the tumor are sampled. This study explored the impact of intra-tumoral heterogeneity in terms of activation/phosphorylation of FDA approved drug targets and downstream kinase substrates. Material and methods: Two independent sets of liver metastases from colorectal cancer were used to evaluate protein kinase-driven signaling networks within different areas using laser capture microdissection and reverse phase protein array. Results: Unsupervised hierarchical clustering analysis indicated that the signaling architecture and activation of the MAPK and AKT-mTOR pathways were consistently maintained within different regions of the same biopsy. Intra-patient variability of the MAPK and AKT-mTOR pathway were <1.06 fold change, while inter-patients variability reached fold change values of 5.01. Conclusions: Protein pathway activation mapping of enriched tumor cells obtained from different regions of the same tumor indicated consistency and robustness independent of the region sampled. This suggests a dominant protein pathway network may be activated in a high percentage of the tumor cell population. Given the genomic intra-tumoral variability, our data suggest that protein/phosphoprotein signaling measurements should be integrated with genomic analysis for precision medicine based analysis.
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Affiliation(s)
- Erika Maria Parasido
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA.,Department of Experimental Oncology, CRO-National Cancer Institute, Aviano, Italy
| | - Alessandra Silvestri
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | | | - Claudio Belluco
- Department of Surgical Oncology, CRO-National Cancer Institute, Aviano, Italy
| | | | - Massimo Milione
- Department of Pathology, Fondazione IRCCS Istituto Nazionale Tumori, Milano, Italy
| | - Flavia Melotti
- Department of Pathology, Fondazione IRCCS Istituto Nazionale Tumori, Milano, Italy
| | - Ruggero De Maria
- Department of Pathology, Sacred Heart Catholic University of Rome, Roma, Italy
| | - Lance Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
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Baldelli E, Calvert V, Hodge A, VanMeter A, Petricoin EF, Pierobon M. Reverse Phase Protein Microarrays. Methods Mol Biol 2018; 1606:149-169. [PMID: 28502000 DOI: 10.1007/978-1-4939-6990-6_11] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
While genes and RNA encode information about cellular status, proteins are considered the engine of the cellular machine, as they are the effective elements that drive all cellular functions including proliferation, migration, differentiation, and apoptosis. Consequently, investigations of the cellular protein network are considered a fundamental tool for understanding cellular functions.Alteration of the cellular homeostasis driven by elaborate intra- and extracellular interactions has become one of the most studied fields in the era of personalized medicine and targeted therapy. Increasing interest has been focused on developing and improving proteomic technologies that are suitable for analysis of clinical samples. In this context, reverse-phase protein microarrays (RPPA) is a sensitive, quantitative, high-throughput immunoassay for protein analyses of tissue samples, cells, and body fluids.RPPA is well suited for broad proteomic profiling and is capable of capturing protein activation as well as biochemical reactions such as phosphorylation, glycosylation, ubiquitination, protein cleavage, and conformational alterations across hundreds of samples using a limited amount of biological material. For these reasons, RPPA represents a valid tool for protein analyses and generates data that help elucidate the functional signaling architecture through protein-protein interaction and protein activation mapping for the identification of critical nodes for individualized or combinatorial targeted therapy.
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Affiliation(s)
- Elisa Baldelli
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, MS 1A9, Manassas, VA, 20110, USA
| | - Valerie Calvert
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, MS 1A9, Manassas, VA, 20110, USA
| | - Alex Hodge
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, MS 1A9, Manassas, VA, 20110, USA
| | - Amy VanMeter
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, MS 1A9, Manassas, VA, 20110, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, MS 1A9, Manassas, VA, 20110, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, MS 1A9, Manassas, VA, 20110, USA.
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Mueller C, Haymond A, Davis JB, Williams A, Espina V. Protein biomarkers for subtyping breast cancer and implications for future research. Expert Rev Proteomics 2018; 15:131-152. [PMID: 29271260 PMCID: PMC6104835 DOI: 10.1080/14789450.2018.1421071] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Breast cancer subtypes are currently defined by a combination of morphologic, genomic, and proteomic characteristics. These subtypes provide a molecular portrait of the tumor that aids diagnosis, prognosis, and treatment escalation/de-escalation options. Gene expression signatures describing intrinsic breast cancer subtypes for predicting risk of recurrence have been rapidly adopted in the clinic. Despite the use of subtype classifications, many patients develop drug resistance, breast cancer recurrence, or therapy failure. Areas covered: This review provides a summary of immunohistochemistry, reverse phase protein array, mass spectrometry, and integrative studies that are revealing differences in biological functions within and between breast cancer subtypes. We conclude with a discussion of rigor and reproducibility for proteomic-based biomarker discovery. Expert commentary: Innovations in proteomics, including implementation of assay guidelines and standards, are facilitating refinement of breast cancer subtypes. Proteomic and phosphoproteomic information distinguish biologically functional subtypes, are predictive of recurrence, and indicate likelihood of drug resistance. Actionable, activated signal transduction pathways can now be quantified and characterized. Proteomic biomarker validation in large, well-designed studies should become a public health priority to capitalize on the wealth of information gleaned from the proteome.
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Affiliation(s)
- Claudius Mueller
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
| | - Amanda Haymond
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
| | - Justin B Davis
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
| | - Alexa Williams
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
| | - Virginia Espina
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
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20
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Castro NP, Golubeva YG. Adaptation of Laser Microdissection Technique to Nanostring RNA Analysis in the Study of a Spontaneous Metastatic Mammary Carcinoma Mouse Model. Methods Mol Biol 2018; 1723:119-137. [PMID: 29344857 DOI: 10.1007/978-1-4939-7558-7_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The mouse model characterized by spontaneous lung metastasis from JygMC (A) cells closely resembles the human triple negative breast cancer (TNBC) subtype. The primary tumors morphologically present both epithelial and spindle-like cells, but metastases in lung parenchyma display only adenocarcinoma properties. In the study of molecular signatures, laser capture microdissection (LCM) on frozen tissue sections was used to separate the following regions of interest: the epithelial-mesenchymal transition (EMT), mesenchymal-epithelial transition (MET), carcinoma, lung metastases, normal mammary gland and normal lung parenchyma. NanoString was selected for the study of molecular signatures in LCM targets as a reliable downstream gene expression platform allowing analysis of tissue lysates without RNA extraction and amplification. This chapter provides detailed protocols for the collection of tissue, LCM sample preparation and dissection, production of lysates, extraction, and quality control of RNA for NanoString analysis, as well as the methodology of Nanostring gene expression profiling experiment.
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Affiliation(s)
- Nadia P Castro
- Tumor Growth Factor Section, Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, USA
| | - Yelena G Golubeva
- Cancer Genomic Research Laboratory (CGR), Division of Cancer Epidemiology and Genetics, NCI, FNLCR, Leidos Biomedical Research, Inc, Gaithersburg, MD, USA.
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21
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Laser Microdissection Workflow for Isolating Nucleic Acids from Fixed and Frozen Tissue Samples. Methods Mol Biol 2018; 1723:33-93. [PMID: 29344854 DOI: 10.1007/978-1-4939-7558-7_3] [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: 12/12/2022]
Abstract
Laser Capture Microdissection has earned a permanent place among modern techniques connecting histology and molecular biology. Laser Capture Microdissection has become an invaluable tool in medical research as a means for collection of specific cell populations isolated from their environment. Such genomic sample enrichment dramatically increases the sensitivity and precision of downstream molecular assays used for biomarker discovery, monitoring disease onset and progression, and in the development of personalized medicine. The diversity of research targets (cancerous and precancerous lesions in clinical and animal research, cell pellets, rodent embryos, frozen tissues, archival repository slides, etc.) and scientific objectives present a challenge in establishing standard protocols for Laser Capture Microdissection. In the present chapter, we share our experiences in design and successful execution of numerous diverse microdissection projects, and provide considerations to be taken into account in planning a microdissection study. Our workflow and protocols are standardized for a wide range of animal and human tissues and adapted to downstream analysis platforms.
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22
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Sereni MI, Baldelli E, Gambara G, Ravaggi A, Hodge KA, Alberts DS, Guillen-Rodriguez JM, Dong T, Memo M, Odicino F, Angioli R, Liotta LA, Pecorelli SL, Petricoin EF, Pierobon M. Kinase-driven metabolic signalling as a predictor of response to carboplatin-paclitaxel adjuvant treatment in advanced ovarian cancers. Br J Cancer 2017; 117:494-502. [PMID: 28664915 PMCID: PMC5558684 DOI: 10.1038/bjc.2017.195] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 05/19/2017] [Accepted: 06/01/2017] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The biological mechanisms underlying early- and advanced-stage epithelial ovarian cancers (EOCs) are still poorly understood. This study explored kinase-driven metabolic signalling in early and advanced EOCs, and its role in tumour progression and response to carboplatin-paclitaxel treatment. METHODS Tumour epithelia were isolated from two independent sets of primary EOC (n=72 and 30 for the discovery and the validation sets, respectively) via laser capture microdissection. Reverse phase protein microarrays were used to broadly profile the kinase-driven metabolic signalling of EOC with particular emphasis on the LBK1-AMPK and AKT-mTOR axes. Signalling activation was compared between early and advanced lesions, and carboplatin-paclitaxel-sensitive and -resistant tumours. RESULTS Advanced EOCs were characterised by a heterogeneous kinase-driven metabolic signature and decreased phosphorylation of the AMPK-AKT-mTOR axis compared to early EOC (P<0.05 for AMPKα T172, AMPKα1 S485, AMPKβ1 S108, AKT S473 and T308, mTOR S2448, p70S6 S371, 4EBP1 S65, GSK-3 α/β S21/9, FOXO1 T24/FOXO3 T32, and FOXO1 S256). Advanced tumours with low relative activation of the metabolic signature and increased FOXO1 T24/FOXO3 T32 phosphorylation (P=0.041) were associated with carboplatin-paclitaxel resistance. CONCLUSIONS If validated in a larger cohort of patients, the decreased AMPK-AKT-mTOR activation and phosphorylation of FOXO1 T24/FOXO3 T32 may help identify carboplatin-paclitaxel-resistant EOC patients.
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Affiliation(s)
- Maria Isabella Sereni
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, Manassas, VA 20110, USA
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
- Department of Obstetrics and Gynecology, Campus Bio-Medico University of Rome, Via Alvaro del Portillo 21, 00128 Roma, Italy
| | - Elisa Baldelli
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, Manassas, VA 20110, USA
| | - Guido Gambara
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, Manassas, VA 20110, USA
| | - Antonella Ravaggi
- Division of Gynecologic Oncology, ‘Angelo Nocivelli’ Institute of Molecular Medicine, University of Brescia, Piazzale Spedali Civili 1, 25123 Brescia, Italy
| | - K Alex Hodge
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, Manassas, VA 20110, USA
| | - David S Alberts
- The University of Arizona Cancer Center, 3838N Campbell Ave, Tucson, AZ 85719, USA
| | | | - Ting Dong
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, Manassas, VA 20110, USA
| | - Maurizio Memo
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Franco Odicino
- Division of Gynecologic Oncology, ‘Angelo Nocivelli’ Institute of Molecular Medicine, University of Brescia, Piazzale Spedali Civili 1, 25123 Brescia, Italy
| | - Roberto Angioli
- Department of Obstetrics and Gynecology, Campus Bio-Medico University of Rome, Via Alvaro del Portillo 21, 00128 Roma, Italy
| | - Lance A Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, Manassas, VA 20110, USA
| | - Sergio L Pecorelli
- Division of Gynecologic Oncology, ‘Angelo Nocivelli’ Institute of Molecular Medicine, University of Brescia, Piazzale Spedali Civili 1, 25123 Brescia, Italy
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, Manassas, VA 20110, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, Manassas, VA 20110, USA
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23
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Labots M, van der Mijn JC, Beekhof R, Piersma SR, de Goeij-de Haas RR, Pham TV, Knol JC, Dekker H, van Grieken NC, Verheul HM, Jiménez CR. Phosphotyrosine-based-phosphoproteomics scaled-down to biopsy level for analysis of individual tumor biology and treatment selection. J Proteomics 2017; 162:99-107. [DOI: 10.1016/j.jprot.2017.04.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 02/28/2017] [Accepted: 04/12/2017] [Indexed: 12/17/2022]
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Pierobon M, Ramos C, Wong S, Hodge KA, Aldrich J, Byron S, Anthony SP, Robert NJ, Northfelt DW, Jahanzeb M, Vocila L, Wulfkuhle J, Gambara G, Gallagher RI, Dunetz B, Hoke N, Dong T, Craig DW, Cristofanilli M, Leyland-Jones B, Liotta LA, O'Shaughnessy JA, Carpten JD, Petricoin EF. Enrichment of PI3K-AKT-mTOR Pathway Activation in Hepatic Metastases from Breast Cancer. Clin Cancer Res 2017; 23:4919-4928. [PMID: 28446508 DOI: 10.1158/1078-0432.ccr-16-2656] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 03/03/2017] [Accepted: 04/18/2017] [Indexed: 12/24/2022]
Abstract
Purpose: Little is known about the molecular signatures associated with specific metastatic sites in breast cancer. Using comprehensive multi-omic molecular profiling, we assessed whether alterations or activation of the PI3K-AKT-mTOR pathway is associated with specific sites of breast cancer metastasis.Experimental Design: Next-generation sequencing-based whole-exome sequencing was coupled with reverse-phase protein microarray (RPPA) functional signaling network analysis to explore the PI3K-AKT-mTOR axis in 32 pretreated breast cancer metastases. RPPA-based signaling data were further validated in an independent cohort of 154 metastatic lesions from breast cancer and 101 unmatched primary breast tumors. The proportion of cases with PI3K-AKT-mTOR genomic alterations or signaling network activation were compared between hepatic and nonhepatic lesions.Results:PIK3CA mutation and activation of AKT (S473) and p70S6K (T389) were detected more frequently among liver metastases than nonhepatic lesions (P < 0.01, P = 0.056, and P = 0.053, respectively). However, PIK3CA mutations alone were insufficient in predicting protein activation (P = 0.32 and P = 0.19 for activated AKT and p70S6K, respectively). RPPA analysis of an independent cohort of 154 tumors confirmed the relationship between pathway activation and hepatic metastasis [AKT (S473), mTOR (S2448), and 4EBP1 (S65); P < 0.01, P = 0.02, and P = 0.01, respectively]. Similar results were also seen between liver metastases and primary breast tumors [AKT (S473) P < 0.01, mTOR (S2448) P < 0.01, 4EBP1 (S65) P = 0.01]. This signature was lost when primary tumors were compared with all metastatic sites combined.Conclusions: Breast cancer patients with liver metastasis may represent a molecularly homogenized cohort with increased incidence of PIK3CA mutations and activation of the PI3K-AKT-mTOR signaling network. Clin Cancer Res; 23(16); 4919-28. ©2017 AACR.
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Affiliation(s)
| | | | - Shukmei Wong
- Translational Genomics Research Institute, Phoenix, Arizona
| | | | | | - Sara Byron
- Translational Genomics Research Institute, Phoenix, Arizona
| | | | | | - Donald W Northfelt
- Division of Hematology/Oncology, Mayo Clinic Arizona, Scottsdale, Arizona
| | - Mohammad Jahanzeb
- University of Miami Sylvester Comprehensive Cancer Center Deerfield Campus, Deerfield Beach, Florida
| | - Linda Vocila
- TD2 Translational Drug Development, Scottsdale, Arizona
| | | | | | | | | | | | - Ting Dong
- George Mason University, Manassas, Virginia
| | - David W Craig
- Translational Genomics Research Institute, Phoenix, Arizona
| | - Massimo Cristofanilli
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois
| | - Brian Leyland-Jones
- Avera Cancer Institute Center for Precision Oncology, Sioux Falls, South Dakota
| | | | | | - John D Carpten
- Translational Genomics Research Institute, Phoenix, Arizona
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25
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Pin E, Stratton S, Belluco C, Liotta L, Nagle R, Hodge KA, Deng J, Dong T, Baldelli E, Petricoin E, Pierobon M. A pilot study exploring the molecular architecture of the tumor microenvironment in human prostate cancer using laser capture microdissection and reverse phase protein microarray. Mol Oncol 2016; 10:1585-1594. [PMID: 27825696 DOI: 10.1016/j.molonc.2016.09.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 09/24/2016] [Accepted: 09/28/2016] [Indexed: 12/24/2022] Open
Abstract
The cross-talk between tumor epithelium and surrounding stromal/immune microenvironment is essential to sustain tumor growth and progression and provides new opportunities for the development of targeted treatments focused on disrupting the tumor ecology. Identification of novel approaches to study these interactions is of primary importance. Using laser capture microdissection (LCM) coupled with reverse phase protein microarray (RPPA) based protein signaling activation mapping we explored the molecular interconnection between tumor epithelium and surrounding stromal microenvironment in 18 prostate cancer (PCa) specimens. Four specimen-matched cellular compartments (normal-appearing epithelium and its adjacent stroma, and malignant epithelium and its adjacent stroma) were isolated for each case. The signaling network analysis of the four compartments unraveled a number of molecular mechanisms underlying the communication between tumor cells and stroma in the context of the tumor microenvironment. In particular, differential expression of inflammatory mediators like IL-8 and IL-10 by the stroma cells appeared to modulate specific cross-talks between the tumor cells and surrounding microenvironment.
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Affiliation(s)
- Elisa Pin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA; Division of Experimental Oncology 2, CRO-IRCCS, National Cancer Institute, Aviano, Italy
| | - Steven Stratton
- Division of Cancer Prevention and Control, University of Arizona Cancer Center, Tucson, AZ, USA
| | - Claudio Belluco
- Department of Surgical Oncology, CRO-IRCCS, National Cancer Institute, Aviano, Italy
| | - Lance Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Ray Nagle
- Division of Cancer Prevention and Control, University of Arizona Cancer Center, Tucson, AZ, USA
| | - K Alex Hodge
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Jianghong Deng
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Ting Dong
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Elisa Baldelli
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Emanuel Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA.
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Lu Y, Ling S, Hegde AM, Byers LA, Coombes K, Mills GB, Akbani R. Using reverse-phase protein arrays as pharmacodynamic assays for functional proteomics, biomarker discovery, and drug development in cancer. Semin Oncol 2016; 43:476-83. [PMID: 27663479 PMCID: PMC5111873 DOI: 10.1053/j.seminoncol.2016.06.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The majority of the targeted therapeutic agents in clinical use target proteins and protein function. Although DNA and RNA analyses have been used extensively to identify novel targets and patients likely to benefit from targeted therapies, these are indirect measures of the levels and functions of most therapeutic targets. More importantly, DNA and RNA analysis is ill-suited for determining the pharmacodynamic effects of target inhibition. Assessing changes in protein levels and function is the most efficient way to evaluate the mechanisms underlying sensitivity and resistance to targeted agents. Understanding these mechanisms is necessary to identify patients likely to benefit from treatment and to develop rational drug combinations to prevent or bypass therapeutic resistance. There is an urgent need for a robust approach to assess protein levels and protein function in model systems and across patient samples. While "shot gun" mass spectrometry can provide in-depth analysis of proteins across a limited number of samples, and emerging approaches such as multiple reaction monitoring have the potential to analyze candidate markers, mass spectrometry has not entered into general use because of the high cost, requirement of extensive analysis and support, and relatively large amount of material needed for analysis. Rather, antibody-based technologies, including immunohistochemistry, radioimmunoassays, enzyme-linked immunosorbent assays (ELISAs), and more recently protein arrays, remain the most common approaches for multiplexed protein analysis. Reverse-phase protein array (RPPA) technology has emerged as a robust, sensitive, cost-effective approach to the analysis of large numbers of samples for quantitative assessment of key members of functional pathways that are affected by tumor-targeting therapeutics. The RPPA platform is a powerful approach for identifying and validating targets, classifying tumor subsets, assessing pharmacodynamics, and identifying prognostic and predictive markers, adaptive responses and rational drug combinations in model systems and patient samples. Its greatest utility has been realized through integration with other analytic platforms such as DNA sequencing, transcriptional profiling, epigenomics, mass spectrometry, and metabolomics. The power of the technology is becoming apparent through its use in pathology laboratories and integration into trial design and implementation.
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Affiliation(s)
- Yiling Lu
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Shiyun Ling
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Apurva M Hegde
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Lauren A Byers
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kevin Coombes
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH
| | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Rehan Akbani
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX.
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Conrads TP, Petricoin EF. The Obama Administration's Cancer Moonshot: A Call for Proteomics. Clin Cancer Res 2016; 22:4556-8. [PMID: 27199492 DOI: 10.1158/1078-0432.ccr-16-0688] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 04/25/2016] [Indexed: 11/16/2022]
Abstract
The Cancer Moonshot Program has been launched and represents a potentially paradigm-shifting initiative with the goal to implement a focused national effort to double the rate of progress against cancer. The placement of precision medicine, immunotherapy, genomics, and combination therapies was placed at the central nexus of this initiative. Although we are extremely enthusiastic about the goals of the program, it is time we meet this revolutionary project with equally bold and cutting-edge ideas: it is time we move firmly into the postgenome era and provide the necessary resources to propel and seize on innovative recent gains in the field of proteomics required for it to stand on equal footing in this narrative as a combined, synergistic engine for molecular profiling. After all, although the genome is the information archive, it is the proteins that actually do the work of the cell and represent the structural cellular machinery. It is the proteins that comprise most of the biomarkers that are measured to detect cancers, constitute the antigens that drive immune response and inter- and intracellular communications, and it is the proteins that are the drug targets for nearly every targeted therapy that is being evaluated in cancer trials today. We believe that a combined systems biology view of the tumor microenvironment that orients cancer studies back to the functional proteome, phosphoproteome, and biochemistry of the cell will be essential to deliver on the promise of the Cancer Moonshot Program. Clin Cancer Res; 22(18); 4556-8. ©2016 AACR.
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Affiliation(s)
- Thomas P Conrads
- Inova Schar Cancer Institute, Inova Center for Personalized Health, Falls Church, Virginia. Gynecologic Cancer Center of Excellence, Annandale, Virginia. The Inova-George Mason University Center for Clinical Proteomics, Manassas, Virginia.
| | - Emanuel F Petricoin
- The Inova-George Mason University Center for Clinical Proteomics, Manassas, Virginia. Center for Applied Proteomics and Molecular Medicine, School of Systems Biology, George Mason University, Manassas, Virginia.
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28
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Castro NP, Merchant AS, Saylor KL, Anver MR, Salomon DS, Golubeva YG. Adaptation of Laser Microdissection Technique for the Study of a Spontaneous Metastatic Mammary Carcinoma Mouse Model by NanoString Technologies. PLoS One 2016; 11:e0153270. [PMID: 27077656 PMCID: PMC4831786 DOI: 10.1371/journal.pone.0153270] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 03/25/2016] [Indexed: 02/07/2023] Open
Abstract
Laser capture microdissection (LCM) of tissue is an established tool in medical research for collection of distinguished cell populations under direct microscopic visualization for molecular analysis. LCM samples have been successfully analyzed in a number of genomic and proteomic downstream molecular applications. However, LCM sample collection and preparation procedure has to be adapted to each downstream analysis platform. In this present manuscript we describe in detail the adaptation of LCM methodology for the collection and preparation of fresh frozen samples for NanoString analysis based on a study of a model of mouse mammary gland carcinoma and its lung metastasis. Our adaptation of LCM sample preparation and workflow to the requirements of the NanoString platform allowed acquiring samples with high RNA quality. The NanoString analysis of such samples provided sensitive detection of genes of interest and their associated molecular pathways. NanoString is a reliable gene expression analysis platform that can be effectively coupled with LCM.
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Affiliation(s)
- Nadia P. Castro
- Tumor Growth Factor Section, Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, 21702, United States of America
| | - Anand S. Merchant
- CCRIFX Bioinformatics Core, National Cancer Institute, Bethesda, MD, 20892, United States of America
| | - Karen L. Saylor
- Tumor Growth Factor Section, Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, 21702, United States of America
| | - Miriam R. Anver
- Pathology-Histotechnology Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, United States of America
| | - David S. Salomon
- Tumor Growth Factor Section, Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, 21702, United States of America
| | - Yelena G. Golubeva
- Pathology-Histotechnology Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, United States of America
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29
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Fredolini C, Byström S, Pin E, Edfors F, Tamburro D, Iglesias MJ, Häggmark A, Hong MG, Uhlen M, Nilsson P, Schwenk JM. Immunocapture strategies in translational proteomics. Expert Rev Proteomics 2015; 13:83-98. [PMID: 26558424 PMCID: PMC4732419 DOI: 10.1586/14789450.2016.1111141] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Aiming at clinical studies of human diseases, antibody-assisted assays have been applied to biomarker discovery and toward a streamlined translation from patient profiling to assays supporting personalized treatments. In recent years, integrated strategies to couple and combine antibodies with mass spectrometry-based proteomic efforts have emerged, allowing for novel possibilities in basic and clinical research. Described in this review are some of the field's current and emerging immunocapture approaches from an affinity proteomics perspective. Discussed are some of their advantages, pitfalls and opportunities for the next phase in clinical and translational proteomics.
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Affiliation(s)
- Claudia Fredolini
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Sanna Byström
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Elisa Pin
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Fredrik Edfors
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Davide Tamburro
- Department of Oncology-Pathology, Clinical Proteomics Mass Spectrometry, SciLifeLab, Karolinska Institutet, Solna, Sweden
| | - Maria Jesus Iglesias
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Anna Häggmark
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Mun-Gwan Hong
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Mathias Uhlen
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Peter Nilsson
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Jochen M Schwenk
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
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