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Alkhatib H, Conage-Pough J, Roy Chowdhury S, Shian D, Zaid D, Rubinstein AM, Sonnenblick A, Peretz-Yablonsky T, Granit A, Carmon E, Kohale IN, Boughey JC, Goetz MP, Wang L, White FM, Kravchenko-Balasha N. Patient-specific signaling signatures predict optimal therapeutic combinations for triple negative breast cancer. Mol Cancer 2024; 23:17. [PMID: 38229082 PMCID: PMC10790458 DOI: 10.1186/s12943-023-01921-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 12/20/2023] [Indexed: 01/18/2024] Open
Abstract
Triple negative breast cancer (TNBC) is a heterogeneous group of tumors which lack estrogen receptor, progesterone receptor, and HER2 expression. Targeted therapies have limited success in treating TNBC, thus a strategy enabling effective targeted combinations is an unmet need. To tackle these challenges and discover individualized targeted combination therapies for TNBC, we integrated phosphoproteomic analysis of altered signaling networks with patient-specific signaling signature (PaSSS) analysis using an information-theoretic, thermodynamic-based approach. Using this method on a large number of TNBC patient-derived tumors (PDX), we were able to thoroughly characterize each PDX by computing a patient-specific set of unbalanced signaling processes and assigning a personalized therapy based on them. We discovered that each tumor has an average of two separate processes, and that, consistent with prior research, EGFR is a major core target in at least one of them in half of the tumors analyzed. However, anti-EGFR monotherapies were predicted to be ineffective, thus we developed personalized combination treatments based on PaSSS. These were predicted to induce anti-EGFR responses or to be used to develop an alternative therapy if EGFR was not present.In-vivo experimental validation of the predicted therapy showed that PaSSS predictions were more accurate than other therapies. Thus, we suggest that a detailed identification of molecular imbalances is necessary to tailor therapy for each TNBC. In summary, we propose a new strategy to design personalized therapy for TNBC using pY proteomics and PaSSS analysis. This method can be applied to different cancer types to improve response to the biomarker-based treatment.
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Affiliation(s)
- Heba Alkhatib
- The Institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, 9103401, Jerusalem, Israel
| | - Jason Conage-Pough
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sangita Roy Chowdhury
- The Institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, 9103401, Jerusalem, Israel
| | - Denen Shian
- The Institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, 9103401, Jerusalem, Israel
| | - Deema Zaid
- The Institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, 9103401, Jerusalem, Israel
| | - Ariel M Rubinstein
- The Institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, 9103401, Jerusalem, Israel
| | - Amir Sonnenblick
- Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tamar Peretz-Yablonsky
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, 9103401, Jerusalem, Israel
| | - Avital Granit
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, 9103401, Jerusalem, Israel
| | - Einat Carmon
- Department of Surgery, Samson Assuta Ashdod University Hospital, Ashdod, Israel
| | - Ishwar N Kohale
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Judy C Boughey
- Department of Surgery, Mayo Clinic, Rochester, MN, 55905, USA
| | - Matthew P Goetz
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Forest M White
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Nataly Kravchenko-Balasha
- The Institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, 9103401, Jerusalem, Israel.
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2
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Kohale IN, Yu J, Zhuang Y, Fan X, Reddy RJ, Sinnwell J, Kalari KR, Boughey JC, Carter JM, Goetz MP, Wang L, White FM. Identification of Src Family Kinases as Potential Therapeutic Targets for Chemotherapy-Resistant Triple Negative Breast Cancer. Cancers (Basel) 2022; 14:cancers14174220. [PMID: 36077757 PMCID: PMC9454481 DOI: 10.3390/cancers14174220] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/16/2022] [Accepted: 08/28/2022] [Indexed: 01/19/2023] Open
Abstract
Neoadjuvant chemotherapy (NAC) remains the cornerstone of the treatment for triple negative breast cancer (TNBC), with the goal of complete eradication of disease. However, for patients with residual disease after NAC, recurrence and mortality rates are high and the identification of novel therapeutic targets is urgently needed. We quantified tyrosine phosphorylation (pTyr)-mediated signaling networks in chemotherapy sensitive (CS) and resistant (CR) TNBC patient-derived xenografts (PDX), to gain novel therapeutic insights. The antitumor activity of SFK inhibition was examined in vivo. Treated tumors were further subjected to phosphoproteomic and RNAseq analysis, to identify the mechanism of actions of the drug. We identified Src Family Kinases (SFKs) as potential therapeutic targets in CR TNBC PDXs. Treatment with dasatinib, an FDA approved SFK inhibitor, led to inhibition of tumor growth in vivo. Further analysis of post-treatment PDXs revealed multiple mechanisms of actions of the drug, confirming the multi-target inhibition of dasatinib. Analysis of pTyr in tumor specimens suggested a low prevalence of SFK-driven tumors, which may provide insight into prior clinical trial results demonstrating a lack of dasatinib antitumor activity in unselected breast cancer patients. Taken together, these results underscore the importance of pTyr characterization of tumors, in identifying new targets, as well as stratifying patients based on their activated signaling networks for therapeutic options. Our data provide a strong rationale for studying SFK inhibitors in biomarker-selected SFK-driven TNBC.
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Affiliation(s)
- Ishwar N. Kohale
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jia Yu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Yongxian Zhuang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Xiaoyang Fan
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Raven J. Reddy
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jason Sinnwell
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Krishna R. Kalari
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Judy C. Boughey
- Department of Surgery, Mayo Clinic, Rochester, MN 55905, USA
| | - Jodi M. Carter
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Matthew P. Goetz
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Forest M. White
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Correspondence: ; Tel.: +617-258-8949
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3
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Hrdina AI, Kohale IN, Kaushal S, Kelly J, Selin NE, Engelward BP, Kroll JH. The Parallel Transformations of Polycyclic Aromatic Hydrocarbons in the Body and in the Atmosphere. Environ Health Perspect 2022; 130:25004. [PMID: 35225689 PMCID: PMC8884122 DOI: 10.1289/ehp9984] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/29/2021] [Accepted: 01/10/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND Polycyclic aromatic hydrocarbons (PAHs) emitted from combustion sources are known to be mutagenic, with more potent species also being carcinogenic. Previous studies show that PAHs can undergo complex transformations both in the body and in the atmosphere, yet these transformation processes are generally investigated separately. OBJECTIVES Drawing from the literature in atmospheric chemistry and toxicology, we highlight the parallel transformations of PAHs that occur in the atmosphere and the body and discuss implications for public health. We also examine key uncertainties related to the toxicity of atmospheric oxidation products of PAHs and explore critical areas for future research. DISCUSSION We focus on a key mode of toxicity for PAHs, in which metabolic processes (driven by cytochrome P450 enzymes), leads to the formation of oxidized PAHs that can damage DNA. Such species can also be formed abiotically in the atmosphere from natural oxidation processes, potentially augmenting PAH toxicity by skipping the necessary metabolic steps that activate their mutagenicity. Despite the large body of literature related to these two general pathways, the extent to which atmospheric oxidation affects a PAH's overall toxicity remains highly uncertain. Combining knowledge and promoting collaboration across both fields can help identify key oxidation pathways and the resulting products that impact public health. CONCLUSIONS Cross-disciplinary research, in which toxicology studies evaluate atmospheric oxidation products and their mixtures, and atmospheric measurements examine the formation of compounds that are known to be most toxic. Close collaboration between research communities can help narrow down which PAHs, and which PAH degradation products, should be targeted when assessing public health risks. https://doi.org/10.1289/EHP9984.
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Affiliation(s)
- Amy I.H. Hrdina
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA
| | - Ishwar N. Kohale
- Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA
| | - Simran Kaushal
- Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Jamie Kelly
- Department of Geography, University College London, London, UK
| | - Noelle E. Selin
- Institute for Data, Systems, and Society, MIT, Cambridge, Massachusetts, USA
- Department of Earth, Atmospheric, and Planetary Sciences, MIT, Cambridge, Massachusetts, USA
| | - Bevin P. Engelward
- Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA
| | - Jesse H. Kroll
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA
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Lopez BGC, Kohale IN, Du Z, Korsunsky I, Abdelmoula WM, Dai Y, Stopka SA, Gaglia G, Randall EC, Regan MS, Basu SS, Clark AR, Marin BM, Mladek AC, Burgenske DM, Agar JN, Supko JG, Grossman SA, Nabors LB, Raychaudhuri S, Ligon KL, Wen PY, Alexander B, Lee EQ, Santagata S, Sarkaria J, White FM, Agar NYR. Multimodal platform for assessing drug distribution and response in clinical trials. Neuro Oncol 2022; 24:64-77. [PMID: 34383057 PMCID: PMC8730776 DOI: 10.1093/neuonc/noab197] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Response to targeted therapy varies between patients for largely unknown reasons. Here, we developed and applied an integrative platform using mass spectrometry imaging (MSI), phosphoproteomics, and multiplexed tissue imaging for mapping drug distribution, target engagement, and adaptive response to gain insights into heterogeneous response to therapy. METHODS Patient-derived xenograft (PDX) lines of glioblastoma were treated with adavosertib, a Wee1 inhibitor, and tissue drug distribution was measured with MALDI-MSI. Phosphoproteomics was measured in the same tumors to identify biomarkers of drug target engagement and cellular adaptive response. Multiplexed tissue imaging was performed on sister sections to evaluate spatial co-localization of drug and cellular response. The integrated platform was then applied on clinical specimens from glioblastoma patients enrolled in the phase 1 clinical trial. RESULTS PDX tumors exposed to different doses of adavosertib revealed intra- and inter-tumoral heterogeneity of drug distribution and integration of the heterogeneous drug distribution with phosphoproteomics and multiplexed tissue imaging revealed new markers of molecular response to adavosertib. Analysis of paired clinical specimens from patients enrolled in the phase 1 clinical trial informed the translational potential of the identified biomarkers in studying patient's response to adavosertib. CONCLUSIONS The multimodal platform identified a signature of drug efficacy and patient-specific adaptive responses applicable to preclinical and clinical drug development. The information generated by the approach may inform mechanisms of success and failure in future early phase clinical trials, providing information for optimizing clinical trial design and guiding future application into clinical practice.
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Affiliation(s)
- Begoña G C Lopez
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ishwar N Kohale
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Ziming Du
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ilya Korsunsky
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Walid M Abdelmoula
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Yang Dai
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Sylwia A Stopka
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Giorgio Gaglia
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Elizabeth C Randall
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael S Regan
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Sankha S Basu
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Amanda R Clark
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Bianca-Maria Marin
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Ann C Mladek
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Jeffrey N Agar
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA
| | - Jeffrey G Supko
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Stuart A Grossman
- Brain Cancer Program, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Louis B Nabors
- University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Keith L Ligon
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Patrick Y Wen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Brian Alexander
- Department of Radiation Oncology, Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Eudocia Q Lee
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Sandro Santagata
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jann Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Forest M White
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Nathalie Y R Agar
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
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5
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Kelly JM, Ivatt PD, Evans MJ, Kroll JH, Hrdina AIH, Kohale IN, White FM, Engelward BP, Selin NE. Global Cancer Risk From Unregulated Polycyclic Aromatic Hydrocarbons. Geohealth 2021; 5:e2021GH000401. [PMID: 34589640 PMCID: PMC8460132 DOI: 10.1029/2021gh000401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 05/26/2023]
Abstract
In assessments of cancer risk from atmospheric polycyclic aromatic hydrocarbons (PAHs), scientists and regulators rarely consider the complex mixture of emitted compounds and degradation products, and they often represent the entire mixture using a single emitted compound-benzo[a]pyrene. Here, we show that benzo[a]pyrene is a poor indicator of PAH risk distribution and management: nearly 90% of cancer risk worldwide results from other PAHs, including unregulated degradation products of emitted PAHs. We develop and apply a global-scale atmospheric model and conduct health impact analyses to estimate human cancer risk from 16 PAHs and several of their N-PAH degradation products. We find that benzo[a]pyrene is a minor contributor to the total cancer risks of PAHs (11%); the remaining risk comes from other directly emitted PAHs (72%) and N-PAHs (17%). We show that assessment and policy-making that relies solely on benzo[a]pyrene exposure provides misleading estimates of risk distribution, the importance of chemical processes, and the prospects for risk mitigation. We conclude that researchers and decision-makers should consider additional PAHs as well as degradation products.
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Affiliation(s)
- Jamie M. Kelly
- Institute for Data, Systems, and SocietyMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Peter D. Ivatt
- Wolfson Atmospheric Chemistry LaboratoriesDepartment of ChemistryUniversity of YorkYorkUK
| | - Mathew J. Evans
- Wolfson Atmospheric Chemistry LaboratoriesDepartment of ChemistryUniversity of YorkYorkUK
- National Centre for Atmospheric ScienceWolfson Atmospheric Chemistry LaboratoriesUniversity of YorkYorkUK
| | - Jesse H. Kroll
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Amy I. H. Hrdina
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Ishwar N. Kohale
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- David H. Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Forest M. White
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- David H. Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMAUSA
- Center for Precision Cancer MedicineMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Bevin P. Engelward
- Center for Precision Cancer MedicineMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Noelle E. Selin
- Institute for Data, Systems, and SocietyMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeMAUSA
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6
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Kohale IN, Burgenske DM, Mladek AC, Bakken KK, Kuang J, Boughey JC, Wang L, Carter JM, Haura EB, Goetz MP, Sarkaria JN, White FM. Quantitative Analysis of Tyrosine Phosphorylation from FFPE Tissues Reveals Patient-Specific Signaling Networks. Cancer Res 2021; 81:3930-3941. [PMID: 34016623 PMCID: PMC8286342 DOI: 10.1158/0008-5472.can-21-0214] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/07/2021] [Accepted: 05/06/2021] [Indexed: 01/07/2023]
Abstract
Human tissue samples commonly preserved as formalin-fixed paraffin-embedded (FFPE) tissues after diagnostic or surgical procedures in the clinic represent an invaluable source of clinical specimens for in-depth characterization of signaling networks to assess therapeutic options. Tyrosine phosphorylation (pTyr) plays a fundamental role in cellular processes and is commonly dysregulated in cancer but has not been studied to date in FFPE samples. In addition, pTyr analysis that may otherwise inform therapeutic interventions for patients has been limited by the requirement for large amounts of frozen tissue. Here we describe a method for highly sensitive, quantitative analysis of pTyr signaling networks, with hundreds of sites quantified from one to two 10-μm sections of FFPE tissue specimens. A combination of optimized magnetic bead-based sample processing, optimized pTyr enrichment strategies, and tandem mass tag multiplexing enabled in-depth coverage of pTyr signaling networks from small amounts of input material. Phosphotyrosine profiles of flash-frozen and FFPE tissues derived from the same tumors suggested that FFPE tissues preserve pTyr signaling characteristics in patient-derived xenografts and archived clinical specimens. pTyr analysis of FFPE tissue sections from breast cancer tumors as well as lung cancer tumors highlighted patient-specific oncogenic driving kinases, indicating potential targeted therapies for each patient. These data suggest the capability for direct translational insight from pTyr analysis of small amounts of FFPE tumor tissue specimens. SIGNIFICANCE: This study reports a highly sensitive method utilizing FFPE tissues to identify dysregulated signaling networks in patient tumors, opening the door for direct translational insights from FFPE tumor tissue banks in hospitals.
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Affiliation(s)
- Ishwar N. Kohale
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | | | - Ann C. Mladek
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | | | - Jenevieve Kuang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | | | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Jodi M. Carter
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Eric B. Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | | | - Jann N. Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Forest M. White
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Corresponding Author: Forest M. White, Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, 76-353, Cambridge, MA 02142. Phone: 617-258-8949; Fax: 617-258-0225; E-mail:
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7
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Kay JE, Corrigan JJ, Armijo AL, Nazari IS, Kohale IN, Torous DK, Avlasevich SL, Croy RG, Wadduwage DN, Carrasco SE, Dertinger SD, White FM, Essigmann JM, Samson LD, Engelward BP. Excision of mutagenic replication-blocking lesions suppresses cancer but promotes cytotoxicity and lethality in nitrosamine-exposed mice. Cell Rep 2021; 34:108864. [PMID: 33730582 PMCID: PMC8527524 DOI: 10.1016/j.celrep.2021.108864] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/05/2021] [Accepted: 02/23/2021] [Indexed: 02/07/2023] Open
Abstract
N-Nitrosodimethylamine (NDMA) is a DNA-methylating agent that has been discovered to contaminate water, food, and drugs. The alkyladenine DNA glycosylase (AAG) removes methylated bases to initiate the base excision repair (BER) pathway. To understand how gene-environment interactions impact disease susceptibility, we study Aag-knockout (Aag-/-) and Aag-overexpressing mice that harbor increased levels of either replication-blocking lesions (3-methyladenine [3MeA]) or strand breaks (BER intermediates), respectively. Remarkably, the disease outcome switches from cancer to lethality simply by changing AAG levels. To understand the underlying basis for this observation, we integrate a suite of molecular, cellular, and physiological analyses. We find that unrepaired 3MeA is somewhat toxic, but highly mutagenic (promoting cancer), whereas excess strand breaks are poorly mutagenic and highly toxic (suppressing cancer and promoting lethality). We demonstrate that the levels of a single DNA repair protein tip the balance between blocks and breaks and thus dictate the disease consequences of DNA damage.
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Affiliation(s)
- Jennifer E Kay
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 01239, USA
| | - Joshua J Corrigan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 01239, USA
| | - Amanda L Armijo
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA 01239, USA
| | - Ilana S Nazari
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 01239, USA
| | - Ishwar N Kohale
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 01239, USA
| | | | | | - Robert G Croy
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 01239, USA
| | - Dushan N Wadduwage
- The John Harvard Distinguished Science Fellows Program, Harvard University, Cambridge, MA 02138, USA; Center for Advanced Imaging, Harvard University, Cambridge, MA 02138, USA
| | - Sebastian E Carrasco
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA 01239, USA
| | | | - Forest M White
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 01239, USA
| | - John M Essigmann
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 01239, USA
| | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 01239, USA
| | - Bevin P Engelward
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 01239, USA.
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