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Wei D, Sun J, Luo Z, Zhang G, Liu Y, Zhang H, Xie Z, Gu Z, Tao WA. Targeted Phosphoproteomics of Human Saliva Extracellular Vesicles via Multiple Reaction Monitoring Cubed (MRM 3). Anal Chem 2024; 96:1223-1231. [PMID: 38205554 DOI: 10.1021/acs.analchem.3c04464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Oral squamous cell carcinoma (OSCC) has become a global health problem due to its increasing incidence and high mortality rate. Early intervention through monitoring of the diagnostic biomarker levels during OSCC treatment is critical. Extracellular vesicles (EVs) are emerging surrogates in intercellular communication through transporting biomolecule cargo and have recently been identified as a potential source of biomarkers such as phosphoproteins for many diseases. Here, we developed a multiple reaction monitoring cubed (MRM3) method coupled with a novel sample preparation strategy, extracellular vesicles to phosphoproteins (EVTOP), to quantify phosphoproteins using a minimal amount of saliva (50 μL) samples from OSCC patients with high specificity and sensitivity. Our results established differential patterns in the phosphopeptide content of healthy, presurgery, and postsurgery OSCC patient groups. Notably, we discovered significantly increased salivary phosphorylated alpha-amylase (AMY) in the postsurgery group compared to the presurgery group. We hereby present the first targeted MS method with extremely high sensitivity for measuring endogenous phosphoproteins in human saliva EVs.
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Affiliation(s)
- Dong Wei
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Jie Sun
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Zhuojun Luo
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Guiyuan Zhang
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Yufeng Liu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Hao Zhang
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Zhuoying Xie
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Zhongze Gu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - W Andy Tao
- Department of Chemistry and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
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2
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Lundeen RA, Kennedy JJ, Murillo OD, Ivey RG, Zhao L, Schoenherr RM, Hoofnagle AN, Wang P, Whiteaker JR, Paulovich AG. Monitoring Both Extended and Tryptic Forms of Stable Isotope-Labeled Standard Peptides Provides an Internal Quality Control of Proteolytic Digestion in Targeted Mass Spectrometry-Based Assays. Mol Cell Proteomics 2023; 22:100621. [PMID: 37478973 PMCID: PMC10458721 DOI: 10.1016/j.mcpro.2023.100621] [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: 04/20/2023] [Revised: 07/10/2023] [Accepted: 07/17/2023] [Indexed: 07/23/2023] Open
Abstract
Targeted mass spectrometry (MS)-based proteomic assays, such as multiplexed multiple reaction monitoring (MRM)-MS assays, enable sensitive and specific quantification of proteotypic peptides as stoichiometric surrogates for proteins. Efforts are underway to expand the use of MRM-MS assays in clinical environments, which requires a reliable strategy to monitor proteolytic digestion efficiency within individual samples. Towards this goal, extended stable isotope-labeled standard (SIS) peptides (hE), which incorporate native proteolytic cleavage sites, can be spiked into protein lysates prior to proteolytic (trypsin) digestion, and release of the tryptic SIS peptide (hT) can be monitored. However, hT measurements alone cannot monitor the extent of digestion and may be confounded by matrix effects specific to individual patient samples; therefore, they are not sufficient to monitor sample-to-sample digestion variability. We hypothesized that measuring undigested hE, along with its paired hT, would improve detection of digestion issues compared to only measuring hT. We tested the ratio of the SIS pair measurements, or hE/hT, as a quality control (QC) metric of trypsin digestion for two MRM assays: a direct-MRM (398 targets) and an immuno-MRM (126 targets requiring immunoaffinity peptide enrichment) assay, with extended SIS peptides observable for 54% (216) and 62% (78) of the targets, respectively. We evaluated the quantitative bias for each target in a series of experiments that adversely affected proteolytic digestion (e.g., variable digestion times, pH, and temperature). We identified a subset of SIS pairs (36 for the direct-MRM, 7 for the immuno-MRM assay) for which the hE/hT ratio reliably detected inefficient digestion that resulted in decreased assay sensitivity and unreliable endogenous quantification. The hE/hT ratio was more responsive to a decrease in digestion efficiency than a metric based on hT measurements alone. For clinical-grade MRM-MS assays, this study describes a ready-to-use QC panel and also provides a road map for designing custom QC panels.
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Affiliation(s)
- Rachel A Lundeen
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Jacob J Kennedy
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Oscar D Murillo
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Richard G Ivey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Lei Zhao
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Regine M Schoenherr
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA; Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Mount Sinai Hospital, New York, New York, USA
| | - Jeffrey R Whiteaker
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA.
| | - Amanda G Paulovich
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA.
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3
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Nguyen HT, Tang W, Webster ALH, Whiteaker JR, Chandler CM, Errazquin R, Roohollahi K, Fritzke M, Hoskins EE, Jonlin E, Wakefield L, Sullivan LB, Chen EY, Dorsman J, Brakenhoff R, Paulovich AG, Grompe M, Garcia-Escudero R, Wells SI, Smogorzewska A, Monnat RJ. Fanconi anemia-isogenic head and neck cancer cell line pairs: A basic and translational science resource. Int J Cancer 2023; 153:183-196. [PMID: 36912284 DOI: 10.1002/ijc.34506] [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: 10/18/2022] [Revised: 01/27/2023] [Accepted: 02/15/2023] [Indexed: 03/14/2023]
Abstract
Fanconi anemia (FA) is a heritable malformation, bone marrow failure and cancer predisposition syndrome that confers an exceptionally high risk of squamous carcinomas. These carcinomas originate in epithelia lining the mouth, proximal esophagus, vulva and anus: their origins are not understood, and no effective ways have been identified to prevent or delay their appearance. Many FA-associated carcinomas are also therapeutically challenging: they may be multi-focal and stage-advanced at diagnosis, and most individuals with FA cannot tolerate standard-of-care systemic therapies such as DNA cross-linking drugs or ionizing radiation due to constitutional DNA damage hypersensitivity. We developed the Fanconi Anemia Cancer Cell Line Resource (FA-CCLR) to foster new work on the origins, treatment and prevention of FA-associated carcinomas. The FA-CCLR consists of Fanconi-isogenic head and neck squamous cell carcinoma (HNSCC) cell line pairs generated from five individuals with FA-associated HNSCC, and five individuals with sporadic HNSCC. Sporadic, isogenic HNSCC cell line pairs were generated in parallel with FA patient-derived isogenic cell line pairs to provide comparable experimental material to use to identify cell and molecular phenotypes driven by germline or somatic loss of Fanconi pathway function, and the subset of these FA-dependent phenotypes that can be modified, complemented or suppressed. All 10 FANC-isogenic cell line pairs are available to academic, non-profit and industry investigators via the "Fanconi Anemia Research Materials" Resource and Repository at Oregon Health & Sciences University, Portland OR.
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Affiliation(s)
- Hiep Tai Nguyen
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Weiliang Tang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Andrew L H Webster
- Laboratory of Genome Maintenance, Rockefeller University, New York, New York, USA
| | - Jeffrey R Whiteaker
- Fred Hutchinson Cancer Center, Clinical Research Division, Seattle, Washington, USA
| | - Christopher M Chandler
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Ricardo Errazquin
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
- Biomedical Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medio-ambientales y Tecnológicas), Madrid, Spain
| | | | - Madeline Fritzke
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | | | - Erica Jonlin
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- University of Washington Institute for Stem Cell and Regenerative Medicine, Seattle, Washington, USA
| | - Leslie Wakefield
- Departments of Pediatrics and Molecular and Medical Genetics, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Lucas B Sullivan
- Fred Hutchinson Cancer Center, Human Biology Division, Seattle, Washington, USA
| | - Eleanor Y Chen
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | | | - Ruud Brakenhoff
- Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Amanda G Paulovich
- Fred Hutchinson Cancer Center, Clinical Research Division, Seattle, Washington, USA
| | - Markus Grompe
- Departments of Pediatrics and Molecular and Medical Genetics, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Ramon Garcia-Escudero
- Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
- Biomedical Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medio-ambientales y Tecnológicas), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Susanne I Wells
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, Rockefeller University, New York, New York, USA
| | - Raymond J Monnat
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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Jurczak W, Elmusharaf N, Fox CP, Townsend W, Paulovich AG, Whiteaker JR, Krantz F, Wun CC, Parr G, Sharma S, Munugalavadla V, Manwani R, Dean E, Munir T. Phase I/II results of ceralasertib as monotherapy or in combination with acalabrutinib in high-risk relapsed/refractory chronic lymphocytic leukemia. Ther Adv Hematol 2023; 14:20406207231173489. [PMID: 37273420 PMCID: PMC10233611 DOI: 10.1177/20406207231173489] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 04/17/2023] [Indexed: 06/06/2023] Open
Abstract
Background Patients with relapsed/refractory (R/R) chronic lymphocytic leukemia (CLL) have limited treatment options. Ceralasertib, a selective ataxia telangiectasia and Rad-3-related protein (ATR) inhibitor, demonstrated synergistic preclinical activity with a Bruton tyrosine kinase (BTK) inhibitor in TP53- and ATM-defective CLL cells. Acalabrutinib is a selective BTK inhibitor approved for treatment of CLL. Objectives To evaluate ceralasertib ± acalabrutinib in R/R CLL. Design Nonrandomized, open-label phase I/II study. Methods In arm A, patients received ceralasertib monotherapy 160 mg twice daily (BID) continuously (cohort 1) or 2 weeks on/2 weeks off (cohort 2). In arm B, patients received acalabrutinib 100 mg BID continuously (cycle 1), followed by combination treatment with ceralasertib 160 mg BID 1 week on/3 weeks off from cycle 2. Co-primary objectives were safety and pharmacokinetics. Efficacy was a secondary objective. Results Eleven patients were treated [arm A, n = 8 (cohort 1, n = 5; cohort 2, n = 3); arm B, n = 3 (acalabrutinib plus ceralasertib, n = 2; acalabrutinib only, n = 1)]. Median duration of exposure was 3.5 and 7.2 months for ceralasertib in arms A and B, respectively, and 15.9 months for acalabrutinib in arm B. Most common grade ⩾3 treatment-emergent adverse events (TEAEs) in arm A were anemia (75%) and thrombocytopenia (63%), with four dose-limiting toxicities (DLTs) of grade 4 thrombocytopenia. No grade ⩾3 TEAEs or DLTs occurred in arm B. Ceralasertib plasma concentrations were similar when administered as monotherapy or in combination. At median follow-up of 15.1 months in arm A, no responses were observed, median progression-free survival (PFS) was 3.8 months, and median overall survival (OS) was 16.9 months. At median follow-up of 17.2 months in arm B, overall response rate was 100%, and median PFS and OS were not reached. Conclusion Ceralasertib alone showed limited clinical benefit. Acalabrutinib plus ceralasertib was tolerable with preliminary activity in patients with R/R CLL, though findings are inconclusive due to small sample size. Registration NCT03328273.
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Affiliation(s)
- Wojciech Jurczak
- Maria Sklodowska-Curie National Institute of
Oncology, Garncarska 11, 31-115 Krakow, Poland
| | | | | | - William Townsend
- NIHR Biomedical Research Centre, University
College London Hospitals NHS Foundation Trust, London, UK
| | | | | | | | | | | | | | | | | | - Emma Dean
- Oncology R&D, AstraZeneca, Cambridge,
UK
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5
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Whiteaker JR, Zhao L, Schoenherr RM, Huang D, Lundeen RA, Voytovich U, Kennedy JJ, Ivey RG, Lin C, Murillo OD, Lorentzen TD, Colantonio S, Caceres TW, Roberts RR, Knotts JG, Reading JJ, Perry CD, Richardson CW, Garcia-Buntley SS, Bocik W, Hewitt SM, Chowdhury S, Vandermeer J, Smith SD, Gopal AK, Ramchurren N, Fling SP, Wang P, Paulovich AG. A multiplexed assay for quantifying immunomodulatory proteins supports correlative studies in immunotherapy clinical trials. Front Oncol 2023; 13:1168710. [PMID: 37205196 PMCID: PMC10185886 DOI: 10.3389/fonc.2023.1168710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 04/10/2023] [Indexed: 05/21/2023] Open
Abstract
Introduction Immunotherapy is an effective treatment for a subset of cancer patients, and expanding the benefits of immunotherapy to all cancer patients will require predictive biomarkers of response and immune-related adverse events (irAEs). To support correlative studies in immunotherapy clinical trials, we are developing highly validated assays for quantifying immunomodulatory proteins in human biospecimens. Methods Here, we developed a panel of novel monoclonal antibodies and incorporated them into a novel, multiplexed, immuno-multiple reaction monitoring mass spectrometry (MRM-MS)-based proteomic assay targeting 49 proteotypic peptides representing 43 immunomodulatory proteins. Results and discussion The multiplex assay was validated in human tissue and plasma matrices, where the linearity of quantification was >3 orders of magnitude with median interday CVs of 8.7% (tissue) and 10.1% (plasma). Proof-of-principle demonstration of the assay was conducted in plasma samples collected in clinical trials from lymphoma patients receiving an immune checkpoint inhibitor. We provide the assays and novel monoclonal antibodies as a publicly available resource for the biomedical community.
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Affiliation(s)
- Jeffrey R. Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Lei Zhao
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Regine M. Schoenherr
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Dongqing Huang
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Rachel A. Lundeen
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Ulianna Voytovich
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Jacob J. Kennedy
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Richard G. Ivey
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Chenwei Lin
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Oscar D. Murillo
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Travis D. Lorentzen
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Simona Colantonio
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Tessa W. Caceres
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Rhonda R. Roberts
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Joseph G. Knotts
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Joshua J. Reading
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Candice D. Perry
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Christopher W. Richardson
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Sandra S. Garcia-Buntley
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - William Bocik
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Stephen M. Hewitt
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, United States
| | - Shrabanti Chowdhury
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jackie Vandermeer
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
- Division of Medical Oncology, Department of Internal Medicine, University of Washington, Seattle, WA, United States
| | - Stephen D. Smith
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
- Division of Medical Oncology, Department of Internal Medicine, University of Washington, Seattle, WA, United States
| | - Ajay K. Gopal
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
- Division of Medical Oncology, Department of Internal Medicine, University of Washington, Seattle, WA, United States
| | - Nirasha Ramchurren
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Steven P. Fling
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Amanda G. Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
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Impact of VALID Act implementation on mass spectrometry-based clinical proteomic laboratory developed tests. J Mass Spectrom Adv Clin Lab 2023; 28:30-34. [PMID: 36865788 PMCID: PMC9971545 DOI: 10.1016/j.jmsacl.2023.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/15/2023] Open
Abstract
Mass spectrometry (MS)-based clinical proteomic Laboratory Developed Tests (LDTs) for the measurement of protein biomarkers related to endocrinology, cardiovascular disease, cancer, and Alzheimer's disease are gaining traction in clinical laboratories due to their value in supporting diagnostic and treatment decisions for patients. Under the current regulatory landscape, MS-based clinical proteomic LDTs are regulated by Clinical Laboratory Improvement Amendments (CLIA) under the auspices of the Centers for Medicaid and Medicare Services (CMS). However, should the Verifying Accurate Leading-Edge In Vitro Clinical Test Development (VALID) Act pass, it will grant the FDA greater authority to oversee diagnostic tests, including LDTs. This could impede clinical laboratories' ability to develop new MS-based proteomic LDTs to support existing and emerging patient care needs. Therefore, this review discusses the currently available MS-based proteomic LDTs and their current regulatory landscape in the context of the potential impacts imposed by the passage of the VALID Act.
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7
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Targeted Quantification of Protein Phosphorylation and Its Contributions towards Mathematical Modeling of Signaling Pathways. Molecules 2023; 28:molecules28031143. [PMID: 36770810 PMCID: PMC9919559 DOI: 10.3390/molecules28031143] [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: 11/18/2022] [Revised: 01/12/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Post-translational modifications (PTMs) are key regulatory mechanisms that can control protein function. Of these, phosphorylation is the most common and widely studied. Because of its importance in regulating cell signaling, precise and accurate measurements of protein phosphorylation across wide dynamic ranges are crucial to understanding how signaling pathways function. Although immunological assays are commonly used to detect phosphoproteins, their lack of sensitivity, specificity, and selectivity often make them unreliable for quantitative measurements of complex biological samples. Recent advances in Mass Spectrometry (MS)-based targeted proteomics have made it a more useful approach than immunoassays for studying the dynamics of protein phosphorylation. Selected reaction monitoring (SRM)-also known as multiple reaction monitoring (MRM)-and parallel reaction monitoring (PRM) can quantify relative and absolute abundances of protein phosphorylation in multiplexed fashions targeting specific pathways. In addition, the refinement of these tools by enrichment and fractionation strategies has improved measurement of phosphorylation of low-abundance proteins. The quantitative data generated are particularly useful for building and parameterizing mathematical models of complex phospho-signaling pathways. Potentially, these models can provide a framework for linking analytical measurements of clinical samples to better diagnosis and treatment of disease.
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8
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Vitanza NA, Wilson AL, Huang W, Seidel K, Brown C, Gustafson JA, Yokoyama JK, Johnson AJ, Baxter BA, Koning RW, Reid AN, Meechan M, Biery MC, Myers C, Rawlings-Rhea SD, Albert CM, Browd SR, Hauptman JS, Lee A, Ojemann JG, Berens ME, Dun MD, Foster JB, Crotty EE, Leary SE, Cole BL, Perez FA, Wright JN, Orentas RJ, Chour T, Newell EW, Whiteaker JR, Zhao L, Paulovich AG, Pinto N, Gust J, Gardner RA, Jensen MC, Park JR. Intraventricular B7-H3 CAR T Cells for Diffuse Intrinsic Pontine Glioma: Preliminary First-in-Human Bioactivity and Safety. Cancer Discov 2023; 13:114-131. [PMID: 36259971 PMCID: PMC9827115 DOI: 10.1158/2159-8290.cd-22-0750] [Citation(s) in RCA: 77] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/13/2022] [Accepted: 10/13/2022] [Indexed: 01/16/2023]
Abstract
Diffuse intrinsic pontine glioma (DIPG) remains a fatal brainstem tumor demanding innovative therapies. As B7-H3 (CD276) is expressed on central nervous system (CNS) tumors, we designed B7-H3-specific chimeric antigen receptor (CAR) T cells, confirmed their preclinical efficacy, and opened BrainChild-03 (NCT04185038), a first-in-human phase I trial administering repeated locoregional B7-H3 CAR T cells to children with recurrent/refractory CNS tumors and DIPG. Here, we report the results of the first three evaluable patients with DIPG (including two who enrolled after progression), who received 40 infusions with no dose-limiting toxicities. One patient had sustained clinical and radiographic improvement through 12 months on study. Patients exhibited correlative evidence of local immune activation and persistent cerebrospinal fluid (CSF) B7-H3 CAR T cells. Targeted mass spectrometry of CSF biospecimens revealed modulation of B7-H3 and critical immune analytes (CD14, CD163, CSF-1, CXCL13, and VCAM-1). Our data suggest the feasibility of repeated intracranial B7-H3 CAR T-cell dosing and that intracranial delivery may induce local immune activation. SIGNIFICANCE This is the first report of repeatedly dosed intracranial B7-H3 CAR T cells for patients with DIPG and includes preliminary tolerability, the detection of CAR T cells in the CSF, CSF cytokine elevations supporting locoregional immune activation, and the feasibility of serial mass spectrometry from both serum and CSF. This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Nicholas A. Vitanza
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington.,Corresponding Author: Nicholas A. Vitanza, Seattle Children's Research Institute, M/S JMB-8, 1900 9th Avenue, Seattle, WA 98101. Phone: 206-884-4084; E-mail:
| | | | - Wenjun Huang
- Seattle Children's Therapeutics, Seattle, Washington
| | - Kristy Seidel
- Seattle Children's Therapeutics, Seattle, Washington
| | - Christopher Brown
- Seattle Children's Therapeutics, Seattle, Washington.,Therapeutic Cell Production Core, Seattle Children's Research Institute, Seattle, Washington
| | | | | | | | | | | | | | - Michael Meechan
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington
| | - Matthew C. Biery
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington
| | - Carrie Myers
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington
| | | | - Catherine M. Albert
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington
| | - Samuel R. Browd
- Division of Neurosurgery, Seattle Children's Hospital and Department of Neurological Surgery, University of Washington, Seattle, Washington
| | - Jason S. Hauptman
- Division of Neurosurgery, Seattle Children's Hospital and Department of Neurological Surgery, University of Washington, Seattle, Washington
| | - Amy Lee
- Division of Neurosurgery, Seattle Children's Hospital and Department of Neurological Surgery, University of Washington, Seattle, Washington
| | - Jeffrey G. Ojemann
- Division of Neurosurgery, Seattle Children's Hospital and Department of Neurological Surgery, University of Washington, Seattle, Washington
| | - Michael E. Berens
- Cancer and Cell Biology Division, The Translational Genomics Research Institute (TGen), Phoenix, Arizona
| | - Matthew D. Dun
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, Callaghan, Australia.,Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, Australia
| | - Jessica B. Foster
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Erin E. Crotty
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington
| | - Sarah E.S. Leary
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington
| | - Bonnie L. Cole
- Department of Laboratories, Seattle Children's Hospital, Seattle, Washington.,Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington
| | - Francisco A. Perez
- Department of Radiology, Seattle Children's Hospital, Seattle, Washington
| | - Jason N. Wright
- Department of Radiology, Seattle Children's Hospital, Seattle, Washington
| | - Rimas J. Orentas
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington
| | - Tony Chour
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Evan W. Newell
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | - Lei Zhao
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Amanda G. Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Navin Pinto
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington
| | - Juliane Gust
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington.,Division of Pediatric Neurology, Department of Neurology, University of Washington, Seattle, Washington
| | - Rebecca A. Gardner
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington.,Seattle Children's Therapeutics, Seattle, Washington
| | | | - Julie R. Park
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington.,Seattle Children's Therapeutics, Seattle, Washington
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9
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Kennedy JJ, Woodcock A, Ivey RG, Lin C, Corral G, Hooper E, Martin G, Longman G, Stancik B, Cromwell EA, Whiteaker JR, Zhao L, Lorentzen TD, Thielman S, Paulovich AG. Preserving the Phosphoproteome of Clinical Biopsies Using a Quick-Freeze Collection Device. Biopreserv Biobank 2022; 20:436-445. [PMID: 36301140 PMCID: PMC9603275 DOI: 10.1089/bio.2022.0068] [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] [Indexed: 11/12/2022] Open
Abstract
There is growing interest in proteomic analyses of tissue biopsies to reveal pathophysiology and identify biomarkers. The current gold standard for collecting tissue biopsies for preserving the proteome and post-translational modifications is flash freezing in liquid nitrogen (LN2). However, in many clinical settings, this is not an option due to unavailability of LN2 nor trained personnel for rapid biospecimen processing. To address this need, we developed a proof-of-concept quick-freeze prototype device to rapidly freeze biospecimens at the point-of-care to preserve the phosphoproteome without the need for LN2. Our objectives were to develop the device, demonstrate the ease of use, confirm the ability to ship through existing cold chain logistics, and evaluate the cooling performance (i.e., cool a tissue sample to <0°C in <60 seconds, below -8°C in <120 seconds, and maintain temperature <0°C for >60 minutes) in the context of preserving the proteome in a tissue biospecimen. To demonstrate feasibility, the performance of the prototype was benchmarked against flash freezing in LN2 using a murine melanoma patient-derived xenograft model subjected to total body irradiation to elicit phosphosignaling in the DNA damage response network. Tumors were harvested and quadrisected, with two parts of the tumor being snap frozen in LN2, and the remaining two parts being rapidly cooled in the prototype quick-freeze biospecimen containers. Phosphoproteins were profiled by liquid chromatography tandem mass spectrometry and quantified by targeted multiple reaction monitoring MS. Overall, the phosphoproteome was equivalent in biospecimens processed using the quick-freeze containers to those using the LN2 gold standard, although the measurements of a subset of phosphopeptides in the device-frozen specimens were more variable than LN2-frozen specimens. The prototype device forms the framework for development of a commercial device that will improve tissue biopsy preservation for measurement of important phosphosignaling molecules.
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Affiliation(s)
- Jacob J. Kennedy
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, Washington, USA
| | | | - Richard G. Ivey
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, Washington, USA
| | - ChenWei Lin
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, Washington, USA
| | - Guy Corral
- Product Creation Studio, Seattle, Washington, USA
| | - Eli Hooper
- Product Creation Studio, Seattle, Washington, USA
| | | | - Gina Longman
- Product Creation Studio, Seattle, Washington, USA
| | | | - Elizabeth A. Cromwell
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, Washington, USA
| | - Jeffrey R. Whiteaker
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, Washington, USA
| | - Lei Zhao
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, Washington, USA
| | - Travis D. Lorentzen
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, Washington, USA
| | | | - Amanda G. Paulovich
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, Washington, USA
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10
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Whiteaker JR, Lundeen RA, Zhao L, Schoenherr RM, Burian A, Huang D, Voytovich U, Wang T, Kennedy JJ, Ivey RG, Lin C, Murillo OD, Lorentzen TD, Thiagarajan M, Colantonio S, Caceres TW, Roberts RR, Knotts JG, Reading JJ, Kaczmarczyk JA, Richardson CW, Garcia-Buntley SS, Bocik W, Hewitt SM, Murray KE, Do N, Brophy M, Wilz SW, Yu H, Ajjarapu S, Boja E, Hiltke T, Rodriguez H, Paulovich AG. Targeted Mass Spectrometry Enables Multiplexed Quantification of Immunomodulatory Proteins in Clinical Biospecimens. Front Immunol 2021; 12:765898. [PMID: 34858420 PMCID: PMC8632241 DOI: 10.3389/fimmu.2021.765898] [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: 08/27/2021] [Accepted: 10/22/2021] [Indexed: 12/11/2022] Open
Abstract
Immunotherapies are revolutionizing cancer care, producing durable responses and potentially cures in a subset of patients. However, response rates are low for most tumors, grade 3/4 toxicities are not uncommon, and our current understanding of tumor immunobiology is incomplete. While hundreds of immunomodulatory proteins in the tumor microenvironment shape the anti-tumor response, few of them can be reliably quantified. To address this need, we developed a multiplex panel of targeted proteomic assays targeting 52 peptides representing 46 proteins using peptide immunoaffinity enrichment coupled to multiple reaction monitoring-mass spectrometry. We validated the assays in tissue and plasma matrices, where performance figures of merit showed over 3 orders of dynamic range and median inter-day CVs of 5.2% (tissue) and 21% (plasma). A feasibility study in clinical biospecimens showed detection of 48/52 peptides in frozen tissue and 38/52 peptides in plasma. The assays are publicly available as a resource for the research community.
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Affiliation(s)
- Jeffrey R. Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Rachel A. Lundeen
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Lei Zhao
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Regine M. Schoenherr
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Aura Burian
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Dongqing Huang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Ulianna Voytovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Tao Wang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Jacob J. Kennedy
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Richard G. Ivey
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Chenwei Lin
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Oscar D. Murillo
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Travis D. Lorentzen
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | | | - Simona Colantonio
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Tessa W. Caceres
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Rhonda R. Roberts
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Joseph G. Knotts
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Joshua J. Reading
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Jan A. Kaczmarczyk
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Christopher W. Richardson
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Sandra S. Garcia-Buntley
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - William Bocik
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Stephen M. Hewitt
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, United States
| | - Karen E. Murray
- Veteran’s Administration (VA) Cooperative Studies Program, Veteran’s Administration (VA) Boston Healthcare System (151MAV), Jamaica Plain, MA, United States
| | - Nhan Do
- Veteran’s Administration (VA) Cooperative Studies Program, Veteran’s Administration (VA) Boston Healthcare System (151MAV), Jamaica Plain, MA, United States
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Mary Brophy
- Veteran’s Administration (VA) Cooperative Studies Program, Veteran’s Administration (VA) Boston Healthcare System (151MAV), Jamaica Plain, MA, United States
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Stephen W. Wilz
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
- Pathology and Laboratory Medicine Service, Program, Veteran’s Administration (VA) Boston Healthcare System, Jamaica Plain, MA, United States
| | - Hongbo Yu
- Pathology and Laboratory Medicine Service, Program, Veteran’s Administration (VA) Boston Healthcare System, Jamaica Plain, MA, United States
- Department of Pathology, Harvard Medical School, Boston, MA, United States
| | - Samuel Ajjarapu
- Veteran’s Administration (VA) Cooperative Studies Program, Veteran’s Administration (VA) Boston Healthcare System (151MAV), Jamaica Plain, MA, United States
- Department of Medicine, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Emily Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, United States
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, United States
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, United States
| | - Amanda G. Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
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11
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Affinity capture in bottom-up protein analysis - Overview of current status of proteolytic peptide capture using antibodies and molecularly imprinted polymers. Anal Chim Acta 2021; 1182:338714. [PMID: 34602193 DOI: 10.1016/j.aca.2021.338714] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/17/2022]
Abstract
Antibody-based affinity capture has become the gold standard in sample preparation for determination of low-abundance protein biomarkers in biological matrices prior to liquid chromatography-mass spectrometry (LC-MS) determination. This comprises both capture of intact proteins prior to the digestion step and capture of proteolytic peptides after digestion of the sample. The latter can be performed both using antibodies specifically developed to capture target proteolytic peptides, as well as by the less explored use of anti-protein antibodies to capture the proteolytic epitope peptide. Molecularly imprinted polymers (MIPs), also called plastic antibodies are another affinity-based approach emerging as sample preparation technique in LC-MS based protein biomarker analysis. The current review gives a critical and comprehensive overview of proteolytic peptide capture using antibodies and MIPs in LC-MS based protein biomarker determination during the last five years. The main emphasis is on capture of non-modified peptides, while a brief overview of affinity capture of peptides containing post-translational modifications (PTMs) is provided.
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12
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Keshishian H, McDonald ER, Mundt F, Melanson R, Krug K, Porter DA, Wallace L, Forestier D, Rabasha B, Marlow SE, Jane‐Valbuena J, Todres E, Specht H, Robinson ML, Jean Beltran PM, Babur O, Olive ME, Golji J, Kuhn E, Burgess M, MacMullan MA, Rejtar T, Wang K, Mani DR, Satpathy S, Gillette MA, Sellers WR, Carr SA. A highly multiplexed quantitative phosphosite assay for biology and preclinical studies. Mol Syst Biol 2021; 17:e10156. [PMID: 34569154 PMCID: PMC8474009 DOI: 10.15252/msb.202010156] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 12/14/2022] Open
Abstract
Reliable methods to quantify dynamic signaling changes across diverse pathways are needed to better understand the effects of disease and drug treatment in cells and tissues but are presently lacking. Here, we present SigPath, a targeted mass spectrometry (MS) assay that measures 284 phosphosites in 200 phosphoproteins of biological interest. SigPath probes a broad swath of signaling biology with high throughput and quantitative precision. We applied the assay to investigate changes in phospho-signaling in drug-treated cancer cell lines, breast cancer preclinical models, and human medulloblastoma tumors. In addition to validating previous findings, SigPath detected and quantified a large number of differentially regulated phosphosites newly associated with disease models and human tumors at baseline or with drug perturbation. Our results highlight the potential of SigPath to monitor phosphoproteomic signaling events and to nominate mechanistic hypotheses regarding oncogenesis, response, and resistance to therapy.
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Affiliation(s)
- Hasmik Keshishian
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMAUSA
| | | | - Filip Mundt
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMAUSA
- Present address:
Novo Nordisk Foundation Center for Protein ResearchFaculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
- Present address:
Department of Oncology and PathologyScience for Life LaboratoryKarolinska InstitutetStockholmSweden
| | - Randy Melanson
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMAUSA
| | - Karsten Krug
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMAUSA
| | - Dale A Porter
- Novartis Institute of Biomedical ResearchCambridgeMAUSA
- Present address:
Cedilla TherapeuticsCambridgeMAUSA
| | - Luke Wallace
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMAUSA
| | - Dominique Forestier
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMAUSA
| | - Bokang Rabasha
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMAUSA
| | - Sara E Marlow
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMAUSA
| | - Judit Jane‐Valbuena
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMAUSA
| | - Ellen Todres
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMAUSA
| | - Harrison Specht
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMAUSA
| | | | | | - Ozgun Babur
- Computer Science DepartmentUniversity of Massachusetts BostonBostonMAUSA
| | - Meagan E Olive
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMAUSA
| | - Javad Golji
- Novartis Institute of Biomedical ResearchCambridgeMAUSA
| | - Eric Kuhn
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMAUSA
| | - Michael Burgess
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMAUSA
| | - Melanie A MacMullan
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMAUSA
| | - Tomas Rejtar
- Novartis Institute of Biomedical ResearchCambridgeMAUSA
| | - Karen Wang
- Novartis Institute of Biomedical ResearchCambridgeMAUSA
| | - DR Mani
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMAUSA
| | - Shankha Satpathy
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMAUSA
| | - Michael A Gillette
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMAUSA
- Division of Pulmonary and Critical Care MedicineMassachusetts General HospitalBostonMAUSA
| | - William R Sellers
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMAUSA
- Department of Medical OncologyDana‐Farber Cancer Institute and Harvard Medical SchoolBostonMAUSA
| | - Steven A Carr
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMAUSA
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13
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Gerritsen JS, White FM. Phosphoproteomics: a valuable tool for uncovering molecular signaling in cancer cells. Expert Rev Proteomics 2021; 18:661-674. [PMID: 34468274 PMCID: PMC8628306 DOI: 10.1080/14789450.2021.1976152] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 08/31/2021] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Many pathologies, including cancer, have been associated with aberrant phosphorylation-mediated signaling networks that drive altered cell proliferation, migration, metabolic regulation, and can lead to systemic inflammation. Phosphoproteomics, the large-scale analysis of protein phosphorylation sites, has emerged as a powerful tool to define signaling network regulation and dysregulation in normal and pathological conditions. AREAS COVERED We provide an overview of methodology for global phosphoproteomics as well as enrichment of specific subsets of the phosphoproteome, including phosphotyrosine and phospho-motif enrichment of kinase substrates. We review quantitative methods, advantages and limitations of different mass spectrometry acquisition formats, and computational approaches to extract biological insight from phosphoproteomics data. Throughout, we discuss various applications and their challenges in implementation. EXPERT OPINION Over the past 20 years the field of phosphoproteomics has advanced to enable deep biological and clinical insight through the quantitative analysis of signaling networks. Future areas of development include Clinical Laboratory Improvement Amendments (CLIA)-approved methods for analysis of clinical samples, continued improvements in sensitivity to enable analysis of small numbers of rare cells and tissue microarrays, and computational methods to integrate data resulting from multiple systems-level quantitative analytical methods.
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Affiliation(s)
- Jacqueline S Gerritsen
- Koch Institute for Integrative Cancer Research; Center for Precision Cancer Medicine; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, U.S.A
| | - Forest M White
- Koch Institute for Integrative Cancer Research; Center for Precision Cancer Medicine; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, U.S.A
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14
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Whiteaker JR, Wang T, Zhao L, Schoenherr RM, Kennedy JJ, Voytovich U, Ivey RG, Huang D, Lin C, Colantonio S, Caceres TW, Roberts RR, Knotts JG, Kaczmarczyk JA, Blonder J, Reading JJ, Richardson CW, Hewitt SM, Garcia-Buntley SS, Bocik W, Hiltke T, Rodriguez H, Harrington EA, Barrett JC, Lombardi B, Marco-Casanova P, Pierce AJ, Paulovich AG. Targeted Mass Spectrometry Enables Quantification of Novel Pharmacodynamic Biomarkers of ATM Kinase Inhibition. Cancers (Basel) 2021; 13:3843. [PMID: 34359745 PMCID: PMC8345163 DOI: 10.3390/cancers13153843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/20/2021] [Accepted: 07/23/2021] [Indexed: 11/16/2022] Open
Abstract
The ATM serine/threonine kinase (HGNC: ATM) is involved in initiation of repair of DNA double-stranded breaks, and ATM inhibitors are currently being tested as anti-cancer agents in clinical trials, where pharmacodynamic (PD) assays are crucial to help guide dose and scheduling and support mechanism of action studies. To identify and quantify PD biomarkers of ATM inhibition, we developed and analytically validated a 51-plex assay (DDR-2) quantifying protein expression and DNA damage-responsive phosphorylation. The median lower limit of quantification was 1.28 fmol, the linear range was over 3 orders of magnitude, the median inter-assay variability was 11% CV, and 86% of peptides were stable for storage prior to analysis. Use of the assay was demonstrated to quantify signaling following ionizing radiation-induced DNA damage in both immortalized lymphoblast cell lines and primary human peripheral blood mononuclear cells, identifying PD biomarkers for ATM inhibition to support preclinical and clinical studies.
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Affiliation(s)
- Jeffrey R. Whiteaker
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA 98109, USA; (J.R.W.); (T.W.); (L.Z.); (R.M.S.); (J.J.K.); (U.V.); (R.G.I.); (D.H.); (C.L.)
| | - Tao Wang
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA 98109, USA; (J.R.W.); (T.W.); (L.Z.); (R.M.S.); (J.J.K.); (U.V.); (R.G.I.); (D.H.); (C.L.)
| | - Lei Zhao
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA 98109, USA; (J.R.W.); (T.W.); (L.Z.); (R.M.S.); (J.J.K.); (U.V.); (R.G.I.); (D.H.); (C.L.)
| | - Regine M. Schoenherr
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA 98109, USA; (J.R.W.); (T.W.); (L.Z.); (R.M.S.); (J.J.K.); (U.V.); (R.G.I.); (D.H.); (C.L.)
| | - Jacob J. Kennedy
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA 98109, USA; (J.R.W.); (T.W.); (L.Z.); (R.M.S.); (J.J.K.); (U.V.); (R.G.I.); (D.H.); (C.L.)
| | - Ulianna Voytovich
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA 98109, USA; (J.R.W.); (T.W.); (L.Z.); (R.M.S.); (J.J.K.); (U.V.); (R.G.I.); (D.H.); (C.L.)
| | - Richard G. Ivey
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA 98109, USA; (J.R.W.); (T.W.); (L.Z.); (R.M.S.); (J.J.K.); (U.V.); (R.G.I.); (D.H.); (C.L.)
| | - Dongqing Huang
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA 98109, USA; (J.R.W.); (T.W.); (L.Z.); (R.M.S.); (J.J.K.); (U.V.); (R.G.I.); (D.H.); (C.L.)
| | - Chenwei Lin
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA 98109, USA; (J.R.W.); (T.W.); (L.Z.); (R.M.S.); (J.J.K.); (U.V.); (R.G.I.); (D.H.); (C.L.)
| | - Simona Colantonio
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA; (S.C.); (T.W.C.); (R.R.R.); (J.G.K.); (J.A.K.); (J.B.); (J.J.R.); (C.W.R.); (S.S.G.-B.); (W.B.)
| | - Tessa W. Caceres
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA; (S.C.); (T.W.C.); (R.R.R.); (J.G.K.); (J.A.K.); (J.B.); (J.J.R.); (C.W.R.); (S.S.G.-B.); (W.B.)
| | - Rhonda R. Roberts
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA; (S.C.); (T.W.C.); (R.R.R.); (J.G.K.); (J.A.K.); (J.B.); (J.J.R.); (C.W.R.); (S.S.G.-B.); (W.B.)
| | - Joseph G. Knotts
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA; (S.C.); (T.W.C.); (R.R.R.); (J.G.K.); (J.A.K.); (J.B.); (J.J.R.); (C.W.R.); (S.S.G.-B.); (W.B.)
| | - Jan A. Kaczmarczyk
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA; (S.C.); (T.W.C.); (R.R.R.); (J.G.K.); (J.A.K.); (J.B.); (J.J.R.); (C.W.R.); (S.S.G.-B.); (W.B.)
| | - Josip Blonder
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA; (S.C.); (T.W.C.); (R.R.R.); (J.G.K.); (J.A.K.); (J.B.); (J.J.R.); (C.W.R.); (S.S.G.-B.); (W.B.)
| | - Joshua J. Reading
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA; (S.C.); (T.W.C.); (R.R.R.); (J.G.K.); (J.A.K.); (J.B.); (J.J.R.); (C.W.R.); (S.S.G.-B.); (W.B.)
| | - Christopher W. Richardson
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA; (S.C.); (T.W.C.); (R.R.R.); (J.G.K.); (J.A.K.); (J.B.); (J.J.R.); (C.W.R.); (S.S.G.-B.); (W.B.)
| | - Stephen M. Hewitt
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD 20892, USA;
| | - Sandra S. Garcia-Buntley
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA; (S.C.); (T.W.C.); (R.R.R.); (J.G.K.); (J.A.K.); (J.B.); (J.J.R.); (C.W.R.); (S.S.G.-B.); (W.B.)
| | - William Bocik
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA; (S.C.); (T.W.C.); (R.R.R.); (J.G.K.); (J.A.K.); (J.B.); (J.J.R.); (C.W.R.); (S.S.G.-B.); (W.B.)
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA; (T.H.); (H.R.)
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA; (T.H.); (H.R.)
| | - Elizabeth A. Harrington
- Translational Sciences, Oncology, AstraZeneca, Cambridge CB4 0WG, UK; (E.A.H.); (J.C.B.); (B.L.); (P.M.-C.); (A.J.P.)
| | - J. Carl Barrett
- Translational Sciences, Oncology, AstraZeneca, Cambridge CB4 0WG, UK; (E.A.H.); (J.C.B.); (B.L.); (P.M.-C.); (A.J.P.)
| | - Benedetta Lombardi
- Translational Sciences, Oncology, AstraZeneca, Cambridge CB4 0WG, UK; (E.A.H.); (J.C.B.); (B.L.); (P.M.-C.); (A.J.P.)
| | - Paola Marco-Casanova
- Translational Sciences, Oncology, AstraZeneca, Cambridge CB4 0WG, UK; (E.A.H.); (J.C.B.); (B.L.); (P.M.-C.); (A.J.P.)
| | - Andrew J. Pierce
- Translational Sciences, Oncology, AstraZeneca, Cambridge CB4 0WG, UK; (E.A.H.); (J.C.B.); (B.L.); (P.M.-C.); (A.J.P.)
| | - Amanda G. Paulovich
- Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA 98109, USA; (J.R.W.); (T.W.); (L.Z.); (R.M.S.); (J.J.K.); (U.V.); (R.G.I.); (D.H.); (C.L.)
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15
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Whiteaker JR, Sharma K, Hoffman MA, Kuhn E, Zhao L, Cocco AR, Schoenherr RM, Kennedy JJ, Voytovich U, Lin C, Fang B, Bowers K, Whiteley G, Colantonio S, Bocik W, Roberts R, Hiltke T, Boja E, Rodriguez H, McCormick F, Holderfield M, Carr SA, Koomen JM, Paulovich AG. Targeted mass spectrometry-based assays enable multiplex quantification of receptor tyrosine kinase, MAP Kinase, and AKT signaling. CELL REPORTS METHODS 2021; 1:100015. [PMID: 34671754 PMCID: PMC8525888 DOI: 10.1016/j.crmeth.2021.100015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/16/2021] [Accepted: 05/07/2021] [Indexed: 02/07/2023]
Abstract
SUMMARY A primary goal of the US National Cancer Institute's Ras initiative at the Frederick National Laboratory for Cancer Research is to develop methods to quantify RAS signaling to facilitate development of novel cancer therapeutics. We use targeted proteomics technologies to develop a community resource consisting of 256 validated multiple reaction monitoring (MRM)-based, multiplexed assays for quantifying protein expression and phosphorylation through the receptor tyrosine kinase, MAPK, and AKT signaling networks. As proof of concept, we quantify the response of melanoma (A375 and SK-MEL-2) and colorectal cancer (HCT-116 and HT-29) cell lines to BRAF inhibition by PLX-4720. These assays replace over 60 Western blots with quantitative mass spectrometry-based assays of high molecular specificity and quantitative precision, showing the value of these methods for pharmacodynamic measurements and mechanism of action studies. Methods, fit-for-purpose validation, and results are publicly available as a resource for the community at assays.cancer.gov. MOTIVATION A lack of quantitative, multiplexable assays for phosphosignaling limits comprehensive investigation of aberrant signaling in cancer and evaluation of novel treatments. To alleviate this limitation, we sought to develop assays using targeted mass spectrometry for quantifying protein expression and phosphorylation through the receptor tyrosine kinase, MAPK, and AKT signaling networks. The resulting assays provide a resource for replacing over 60 Western blots in examining cancer signaling and tumor biology with high molecular specificity and quantitative rigor.
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Affiliation(s)
- Jeffrey R. Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kanika Sharma
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Melissa A. Hoffman
- Proteomics and Metabolomics Core, Department of Molecular Oncology, and Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Eric Kuhn
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Lei Zhao
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Alexandra R. Cocco
- Gillings School of Global Public Health, Kenan-Flagler Business School, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Regine M. Schoenherr
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jacob J. Kennedy
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ulianna Voytovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Chenwei Lin
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Bin Fang
- Proteomics and Metabolomics Core, Department of Molecular Oncology, and Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Kiah Bowers
- Proteomics and Metabolomics Core, Department of Molecular Oncology, and Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Gordon Whiteley
- Antibody Characterization Laboratory, Leidos Biochemical Research Inc, Frederick National Laboratory for Cancer Research ATRF, Frederick, MD 21701, USA
| | - Simona Colantonio
- Antibody Characterization Laboratory, Leidos Biochemical Research Inc, Frederick National Laboratory for Cancer Research ATRF, Frederick, MD 21701, USA
| | - William Bocik
- Antibody Characterization Laboratory, Leidos Biochemical Research Inc, Frederick National Laboratory for Cancer Research ATRF, Frederick, MD 21701, USA
| | - Rhonda Roberts
- Antibody Characterization Laboratory, Leidos Biochemical Research Inc, Frederick National Laboratory for Cancer Research ATRF, Frederick, MD 21701, USA
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Emily Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Frank McCormick
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Matthew Holderfield
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
- Department of Biology, Revolution Medicines, Inc., Redwood City, CA 94063, USA
| | - Steven A. Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - John M. Koomen
- Proteomics and Metabolomics Core, Department of Molecular Oncology, and Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Amanda G. Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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16
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Liu Q, Palomero L, Moore J, Guix I, Espín R, Aytés A, Mao JH, Paulovich AG, Whiteaker JR, Ivey RG, Iliakis G, Luo D, Chalmers AJ, Murnane J, Pujana MA, Barcellos-Hoff MH. Loss of TGFβ signaling increases alternative end-joining DNA repair that sensitizes to genotoxic therapies across cancer types. Sci Transl Med 2021; 13:eabc4465. [PMID: 33568520 PMCID: PMC8208885 DOI: 10.1126/scitranslmed.abc4465] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 12/07/2020] [Indexed: 12/17/2022]
Abstract
Among the pleotropic roles of transforming growth factor-β (TGFβ) signaling in cancer, its impact on genomic stability is least understood. Inhibition of TGFβ signaling increases use of alternative end joining (alt-EJ), an error-prone DNA repair process that typically functions as a "backup" pathway if double-strand break repair by homologous recombination or nonhomologous end joining is compromised. However, the consequences of this functional relationship on therapeutic vulnerability in human cancer remain unknown. Here, we show that TGFβ broadly controls the DNA damage response and suppresses alt-EJ genes that are associated with genomic instability. Mechanistically based TGFβ and alt-EJ gene expression signatures were anticorrelated in glioblastoma, squamous cell lung cancer, and serous ovarian cancer. Consistent with error-prone repair, more of the genome was altered in tumors classified as low TGFβ and high alt-EJ, and the corresponding patients had better outcomes. Pan-cancer analysis of solid neoplasms revealed that alt-EJ genes were coordinately expressed and anticorrelated with TGFβ competency in 16 of 17 cancer types tested. Moreover, regardless of cancer type, tumors classified as low TGFβ and high alt-EJ were characterized by an insertion-deletion mutation signature containing short microhomologies and were more sensitive to genotoxic therapy. Collectively, experimental studies revealed that loss or inhibition of TGFβ signaling compromises the DNA damage response, resulting in ineffective repair by alt-EJ. Translation of this mechanistic relationship into gene expression signatures identified a robust anticorrelation that predicts response to genotoxic therapies, thereby expanding the potential therapeutic scope of TGFβ biology.
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Affiliation(s)
- Qi Liu
- Department of Radiation Oncology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA
| | - Luis Palomero
- ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona 08908, Catalonia, Spain
| | - Jade Moore
- Department of Radiation Oncology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA
| | - Ines Guix
- Department of Radiation Oncology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA
| | - Roderic Espín
- ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona 08908, Catalonia, Spain
| | - Alvaro Aytés
- ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona 08908, Catalonia, Spain
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Amanda G Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jeffrey R Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Richard G Ivey
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - George Iliakis
- Institute of Medical Radiation Biology, University of Duisburg-Essen, University Hospital Essen, Essen 45147, Germany
| | - Daxian Luo
- Institute of Medical Radiation Biology, University of Duisburg-Essen, University Hospital Essen, Essen 45147, Germany
| | - Anthony J Chalmers
- Institute of Cancer Sciences and Beatson West of Scotland Cancer Centre, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
| | - John Murnane
- Department of Radiation Oncology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA
| | - Miquel Angel Pujana
- ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona 08908, Catalonia, Spain.
| | - Mary Helen Barcellos-Hoff
- Department of Radiation Oncology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA.
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17
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Petralia F, Tignor N, Reva B, Koptyra M, Chowdhury S, Rykunov D, Krek A, Ma W, Zhu Y, Ji J, Calinawan A, Whiteaker JR, Colaprico A, Stathias V, Omelchenko T, Song X, Raman P, Guo Y, Brown MA, Ivey RG, Szpyt J, Guha Thakurta S, Gritsenko MA, Weitz KK, Lopez G, Kalayci S, Gümüş ZH, Yoo S, da Veiga Leprevost F, Chang HY, Krug K, Katsnelson L, Wang Y, Kennedy JJ, Voytovich UJ, Zhao L, Gaonkar KS, Ennis BM, Zhang B, Baubet V, Tauhid L, Lilly JV, Mason JL, Farrow B, Young N, Leary S, Moon J, Petyuk VA, Nazarian J, Adappa ND, Palmer JN, Lober RM, Rivero-Hinojosa S, Wang LB, Wang JM, Broberg M, Chu RK, Moore RJ, Monroe ME, Zhao R, Smith RD, Zhu J, Robles AI, Mesri M, Boja E, Hiltke T, Rodriguez H, Zhang B, Schadt EE, Mani DR, Ding L, Iavarone A, Wiznerowicz M, Schürer S, Chen XS, Heath AP, Rokita JL, Nesvizhskii AI, Fenyö D, Rodland KD, Liu T, Gygi SP, Paulovich AG, Resnick AC, Storm PB, Rood BR, Wang P. Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer. Cell 2020; 183:1962-1985.e31. [PMID: 33242424 PMCID: PMC8143193 DOI: 10.1016/j.cell.2020.10.044] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 06/19/2020] [Accepted: 10/26/2020] [Indexed: 02/06/2023]
Abstract
We report a comprehensive proteogenomics analysis, including whole-genome sequencing, RNA sequencing, and proteomics and phosphoproteomics profiling, of 218 tumors across 7 histological types of childhood brain cancer: low-grade glioma (n = 93), ependymoma (32), high-grade glioma (25), medulloblastoma (22), ganglioglioma (18), craniopharyngioma (16), and atypical teratoid rhabdoid tumor (12). Proteomics data identify common biological themes that span histological boundaries, suggesting that treatments used for one histological type may be applied effectively to other tumors sharing similar proteomics features. Immune landscape characterization reveals diverse tumor microenvironments across and within diagnoses. Proteomics data further reveal functional effects of somatic mutations and copy number variations (CNVs) not evident in transcriptomics data. Kinase-substrate association and co-expression network analysis identify important biological mechanisms of tumorigenesis. This is the first large-scale proteogenomics analysis across traditional histological boundaries to uncover foundational pediatric brain tumor biology and inform rational treatment selection.
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Affiliation(s)
- Francesca Petralia
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nicole Tignor
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Boris Reva
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mateusz Koptyra
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Shrabanti Chowdhury
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dmitry Rykunov
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Weiping Ma
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yuankun Zhu
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jiayi Ji
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anna Calinawan
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Antonio Colaprico
- Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Vasileios Stathias
- Department of Pharmacology, Institute for Data Science and Computing, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33146, USA
| | - Tatiana Omelchenko
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xiaoyu Song
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Pichai Raman
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yiran Guo
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Miguel A Brown
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Richard G Ivey
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - John Szpyt
- Thermo Fisher Scientific Center for Multiplexed Proteomics, Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sanjukta Guha Thakurta
- Thermo Fisher Scientific Center for Multiplexed Proteomics, Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Karl K Weitz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Gonzalo Lopez
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Selim Kalayci
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Seungyeul Yoo
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Hui-Yin Chang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Karsten Krug
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02412, USA
| | - Lizabeth Katsnelson
- Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Ying Wang
- Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jacob J Kennedy
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Lei Zhao
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Krutika S Gaonkar
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Brian M Ennis
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Bo Zhang
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Valerie Baubet
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lamiya Tauhid
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jena V Lilly
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jennifer L Mason
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Bailey Farrow
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nathan Young
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sarah Leary
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Cancer and Blood Disorders Center, Seattle Children's Hospital, Seattle, WA 98105, USA; Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Jamie Moon
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Javad Nazarian
- Children's National Research Institute, George Washington University School of Medicine, Washington, DC 20010, USA; Department of Oncology, Children's Research Center, University Children's Hospital Zürich, Zürich 8032, Switzerland
| | - Nithin D Adappa
- Department of Otorhinolaryngology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James N Palmer
- Department of Otorhinolaryngology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert M Lober
- Department of Neurosurgery, Dayton Children's Hospital, Dayton, OH 45404, USA
| | - Samuel Rivero-Hinojosa
- Children's National Research Institute, George Washington University School of Medicine, Washington, DC 20010, USA
| | - Liang-Bo Wang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Joshua M Wang
- Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Matilda Broberg
- Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Rosalie K Chu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Rui Zhao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Jun Zhu
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Emily Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02412, USA
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 631110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Antonio Iavarone
- Institute for Cancer Genetics, Department of Neurology, Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Maciej Wiznerowicz
- Poznan University of Medical Sciences, 61-701 Poznań, Poland; International Institute for Molecular Oncology, 61-203 Poznań, Poland
| | - Stephan Schürer
- Department of Pharmacology, Institute for Data Science and Computing, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33146, USA
| | - Xi S Chen
- Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Allison P Heath
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jo Lynne Rokita
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - David Fenyö
- Institute for Systems Genetics; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR 97221, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Steven P Gygi
- Thermo Fisher Scientific Center for Multiplexed Proteomics, Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Adam C Resnick
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Phillip B Storm
- Center for Data-Driven Discovery in Biomedicine, Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Brian R Rood
- Children's National Research Institute, George Washington University School of Medicine, Washington, DC 20010, USA.
| | - Pei Wang
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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18
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Liu K, Singer E, Cohn W, Micewicz ED, McBride WH, Whitelegge JP, Loo JA. Time-Dependent Measurement of Nrf2-Regulated Antioxidant Response to Ionizing Radiation Toward Identifying Potential Protein Biomarkers for Acute Radiation Injury. Proteomics Clin Appl 2019; 13:e1900035. [PMID: 31419066 PMCID: PMC7213060 DOI: 10.1002/prca.201900035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/16/2019] [Indexed: 01/06/2023]
Abstract
PURPOSE Potential acute exposure to ionizing radiation in nuclear or radiological accidents presents complex mass casualty scenarios that demand prompt triage and treatment decisions. Due to delayed symptoms and varied response of radiation victims, there is an urgent need to develop robust biomarkers to assess the extent of injuries in individuals. EXPERIMENTAL DESIGN The transcription factor Nrf2 is the master of redox homeostasis and there is transcriptional evidence of Nrf2-dependent antioxidant response activation upon radiation. The biomarker potential of Nrf2-dependent downstream target enzymes is investigated by measuring their response in bone marrow extracted from C57Bl/6 and C3H mice of both genders for up to 4 days following 6 Gy total body irradiation using targeted MS. RESULTS Overall, C57Bl/6 mice have a stronger proteomic response than C3H mice. In both strains, male mice have more occurrences of upregulation in antioxidant enzymes than female mice. For C57Bl/6 male mice, three proteins show elevated abundances after radiation exposure: catalase, superoxide dismutase 1, and heme oxygenase 1. Across both strains and genders, glutathione S-transferase Mu 1 is consistently decreased. CONCLUSIONS AND CLINICAL RELEVANCE This study provides the basis for future development of organ-specific protein biomarkers used in diagnostic blood test for radiation injury.
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Affiliation(s)
- Kate Liu
- Department of Chemistry and Biochemistry, UCLA
| | - Elizabeth Singer
- Pasarow Mass Spectrometry Laboratory, Jane and Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, UCLA
| | - Whitaker Cohn
- Pasarow Mass Spectrometry Laboratory, Jane and Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, UCLA
| | - Ewa D. Micewicz
- Pasarow Mass Spectrometry Laboratory, Jane and Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, UCLA
| | | | - Julian P. Whitelegge
- Pasarow Mass Spectrometry Laboratory, Jane and Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, UCLA
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, UCLA
- Department of Biological Chemistry, David Geffen School of Medicine, Molecular Biology Institute, and UCLA/DOE Institute for Genomics and Proteomics, UCLA
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19
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Zhang B, Whiteaker JR, Hoofnagle AN, Baird GS, Rodland KD, Paulovich AG. Clinical potential of mass spectrometry-based proteogenomics. Nat Rev Clin Oncol 2019; 16:256-268. [PMID: 30487530 PMCID: PMC6448780 DOI: 10.1038/s41571-018-0135-7] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cancer genomics research aims to advance personalized oncology by finding and targeting specific genetic alterations associated with cancers. In genome-driven oncology, treatments are selected for individual patients on the basis of the findings of tumour genome sequencing. This personalized approach has prolonged the survival of subsets of patients with cancer. However, many patients do not respond to the predicted therapies based on the genomic profiles of their tumours. Furthermore, studies pairing genomic and proteomic analyses of samples from the same tumours have shown that the proteome contains novel information that cannot be discerned through genomic analysis alone. This observation has led to the concept of proteogenomics, in which both types of data are leveraged for a more complete view of tumour biology that might enable patients to be more successfully matched to effective treatments than they would using genomics alone. In this Perspective, we discuss the added value of proteogenomics over the current genome-driven approach to the clinical characterization of cancers and summarize current efforts to incorporate targeted proteomic measurements based on selected/multiple reaction monitoring (SRM/MRM) mass spectrometry into the clinical laboratory to facilitate clinical proteogenomics.
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Affiliation(s)
- Bing Zhang
- Department of Molecular and Human Genetics, Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Jeffrey R Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Andrew N Hoofnagle
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Geoffrey S Baird
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Cell, Development and Cancer Biology, Oregon Health & Sciences University, Portland, OR, USA
| | - Amanda G Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Division of Medical Oncology, University of Washington School of Medicine, Seattle, WA, USA.
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20
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Lorentzian A, Uzozie A, Lange PF. Origins and clinical relevance of proteoforms in pediatric malignancies. Expert Rev Proteomics 2019; 16:185-200. [PMID: 30700156 DOI: 10.1080/14789450.2019.1575206] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Cancer changes the proteome in complex ways that reach well beyond simple changes in protein abundance. Genomic and transcriptional variations and post-translational protein modification create functional variants of a protein, known as proteoforms. Childhood cancers have fewer genomic alterations but show equally dramatic phenotypic changes as malignant cells in adults. Therefore, unraveling the complexities of the proteome is even more important in pediatric malignancies. Areas covered: In this review, the biological origins of proteoforms and technological advancements in the study of proteoforms are discussed. Particular emphasis is given to their implication in childhood malignancies and the critical role of cancer-specific proteoforms for the next generation of cancer therapies and diagnostics. Expert opinion: Recent advancements in technology have led to a better understanding of the underlying mechanisms of tumorigenesis. This has been critical for the development of more effective and less harmful treatments that are based on direct targeting of altered proteins and deregulated pathways. As proteome coverage and the ability to detect complex proteoforms increase, the most need for change is in data compilation and database availability to mediate high-level data analysis and allow for better functional annotation of proteoforms.
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Affiliation(s)
- Amanda Lorentzian
- a Department of Cell and Developmental Biology , University of British Columbia , Vancouver , BC , Canada.,b Michael Cuccione Childhood Cancer Research Program , BC Children's Hospital Research Institute , Vancouver , BC , Canada
| | - Anuli Uzozie
- b Michael Cuccione Childhood Cancer Research Program , BC Children's Hospital Research Institute , Vancouver , BC , Canada.,c Department of Pathology and Laboratory Medicine , University of British Columbia , Vancouver , BC , Canada
| | - Philipp F Lange
- a Department of Cell and Developmental Biology , University of British Columbia , Vancouver , BC , Canada.,b Michael Cuccione Childhood Cancer Research Program , BC Children's Hospital Research Institute , Vancouver , BC , Canada.,c Department of Pathology and Laboratory Medicine , University of British Columbia , Vancouver , BC , Canada
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21
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Ryan DJ, Spraggins JM, Caprioli RM. Protein identification strategies in MALDI imaging mass spectrometry: a brief review. Curr Opin Chem Biol 2019; 48:64-72. [PMID: 30476689 PMCID: PMC6382520 DOI: 10.1016/j.cbpa.2018.10.023] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/26/2018] [Accepted: 10/26/2018] [Indexed: 01/21/2023]
Abstract
Matrix assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) is a powerful technology used to investigate the spatial distributions of thousands of molecules throughout a tissue section from a single experiment. As proteins represent an important group of functional molecules in tissue and cells, the imaging of proteins has been an important point of focus in the development of IMS technologies and methods. Protein identification is crucial for the biological contextualization of molecular imaging data. However, gas-phase fragmentation efficiency of MALDI generated proteins presents significant challenges, making protein identification directly from tissue difficult. This review highlights methods and technologies specifically related to protein identification that have been developed to overcome these challenges in MALDI IMS experiments.
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Affiliation(s)
- Daniel J. Ryan
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
| | - Jeffrey M. Spraggins
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, TN 37205, USA
| | - Richard M. Caprioli
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
- Mass Spectrometry Research Center, Vanderbilt University, 465 21 Ave S #9160, Nashville, TN 37235, USA
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, TN 37205, USA
- Department of Pharmacology, Vanderbilt University, 442 Robinson Research Building, 2220 Pierce Avenue, Nashville, TN 37232, USA
- Department of Medicine, Vanderbilt University, 465 21 Ave #9160, Nashville, TN 37235, USA
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22
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pRAD50: a novel and clinically applicable pharmacodynamic biomarker of both ATM and ATR inhibition identified using mass spectrometry and immunohistochemistry. Br J Cancer 2018; 119:1233-1243. [PMID: 30385821 PMCID: PMC6251026 DOI: 10.1038/s41416-018-0286-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 08/17/2018] [Accepted: 09/11/2018] [Indexed: 01/26/2023] Open
Abstract
Background AZD0156 and AZD6738 are potent and selective inhibitors of ataxia-telangiectasia-kinase (ATM) and ataxia-telangiectasia-mutated and Rad3-related (ATR), respectively, important sensors/signallers of DNA damage. Methods We used multiplexed targeted-mass-spectrometry to select pRAD50(Ser635) as a pharmacodynamic biomarker for AZD0156-mediated ATM inhibition from a panel of 45 peptides, then developed and tested a clinically applicable immunohistochemistry assay for pRAD50(Ser635) detection in FFPE tissue. Results We found moderate pRAD50 baseline levels across cancer indications. pRAD50 was detectable in 100% gastric cancers (n = 23), 99% colorectal cancers (n = 102), 95% triple-negative-breast cancers (TNBC) (n = 40) and 87.5% glioblastoma-multiformes (n = 16). We demonstrated AZD0156 target inhibition in TNBC patient-derived xenograft models; where AZD0156 monotherapy or post olaparib treatment, resulted in a 34–72% reduction in pRAD50. Similar inhibition of pRAD50 (68%) was observed following ATM inhibitor treatment post irinotecan in a colorectal cancer xenograft model. ATR inhibition, using AZD6738, increased pRAD50 in the ATM-proficient models whilst in ATM-deficient models the opposite was observed, suggesting pRAD50 pharmacodynamics post ATR inhibition may be ATM-dependent and could be useful to determine ATM functionality in patients treated with ATR inhibitors. Conclusion Together these data support clinical utilisation of pRAD50 as a biomarker of AZD0156 and AZD6738 pharmacology to elucidate clinical pharmacokinetic/pharmacodynamic relationships, thereby informing recommended Phase 2 dose/schedule.
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23
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Whiteaker JR, Zhao L, Ivey RG, Sanchez-Bonilla M, Moore HD, Schoenherr RM, Yan P, Lin C, Shimamura A, Paulovich AG. Targeted mass spectrometry enables robust quantification of FANCD2 mono-ubiquitination in response to DNA damage. DNA Repair (Amst) 2018; 65:47-53. [PMID: 29605812 DOI: 10.1016/j.dnarep.2018.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 03/19/2018] [Accepted: 03/19/2018] [Indexed: 12/28/2022]
Abstract
The Fanconi anemia pathway is an important coordinator of DNA repair pathways and is particularly relevant to repair of DNA inter-strand crosslinks. Central to the pathway is monoubiquitination of FANCD2, requiring the function of multiple proteins in an upstream Fanconi core complex. We present development and analytical characterization of a novel assay for quantification of unmodified and monoubiquitinated FANCD2 proteoforms, based on peptide immunoaffinity enrichment and targeted multiple reaction monitoring mass spectrometry (immuno-MRM). The immuno-MRM assay is analytically characterized using fit-for-purpose method validation. The assay linear range is >3 orders of magnitude with total repeatability <16% CV. In proof-of-principle experiments, we demonstrate application of the multiplex assay by quantifying the FANCD2 proteoforms following mitomycin-c treatment in an isogenic pair of FancA-corrected and uncorrected cell lines, as well as primary peripheral blood mononuclear cells from Fanconi Anemia patients. Additionally, we demonstrate detection of endogenous FANCD2 monoubiquitination in human breast cancer tissue. The immuno-MRM assay provides a potential functional diagnostic for patients with Fanconi Anemia with defects in the upstream FA complex or FANCD2, and a potential test for predicting sensitivity to DNA cross-linking agents in human cancers.
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Affiliation(s)
- Jeffrey R Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, United States
| | - Lei Zhao
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, United States
| | - Richard G Ivey
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, United States
| | - Marilyn Sanchez-Bonilla
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, United States; Seattle Children's Research Institute, Seattle, WA, United States
| | - Heather D Moore
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, United States
| | - Regine M Schoenherr
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, United States
| | - Ping Yan
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, United States
| | - Chenwei Lin
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, United States
| | - Akiko Shimamura
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, United States
| | - Amanda G Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, United States.
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