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Zhou Z, Zhang R, Zhou A, Lv J, Chen S, Zou H, Zhang G, Lin T, Wang Z, Zhang Y, Weng S, Han X, Liu Z. Proteomics appending a complementary dimension to precision oncotherapy. Comput Struct Biotechnol J 2024; 23:1725-1739. [PMID: 38689716 PMCID: PMC11058087 DOI: 10.1016/j.csbj.2024.04.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
Recent advances in high-throughput proteomic profiling technologies have facilitated the precise quantification of numerous proteins across multiple specimens concurrently. Researchers have the opportunity to comprehensively analyze the molecular signatures in plentiful medical specimens or disease pattern cell lines. Along with advances in data analysis and integration, proteomics data could be efficiently consolidated and employed to recognize precise elementary molecular mechanisms and decode individual biomarkers, guiding the precision treatment of tumors. Herein, we review a broad array of proteomics technologies and the progress and methods for the integration of proteomics data and further discuss how to better merge proteomics in precision medicine and clinical settings.
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Affiliation(s)
- Zhaokai Zhou
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan 450052, China
| | - Ruiqi Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Aoyang Zhou
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Jinxiang Lv
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Shuang Chen
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Haijiao Zou
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Ge Zhang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Ting Lin
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Zhan Wang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan 450052, China
| | - Yuyuan Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Siyuan Weng
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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Lang JD, Nguyen TVV, Levin MK, Blas PE, Williams HL, Rodriguez ESR, Briones N, Mueller C, Selleck W, Moore S, Zismann VL, Hendricks WPD, Espina V, O'Shaughnessy J. Pilot clinical trial and phenotypic analysis in chemotherapy-pretreated, metastatic triple-negative breast cancer patients treated with oral TAK-228 and TAK-117 (PIKTOR) to increase DNA damage repair deficiency followed by cisplatin and nab paclitaxel. Biomark Res 2023; 11:73. [PMID: 37491309 PMCID: PMC10369813 DOI: 10.1186/s40364-023-00511-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/04/2023] [Indexed: 07/27/2023] Open
Abstract
BACKGROUND A subset of triple-negative breast cancers (TNBCs) have homologous recombination deficiency with upregulation of compensatory DNA repair pathways. PIKTOR, a combination of TAK-228 (TORC1/2 inhibitor) and TAK-117 (PI3Kα inhibitor), is hypothesized to increase genomic instability and increase DNA damage repair (DDR) deficiency, leading to increased sensitivity to DNA-damaging chemotherapy and to immune checkpoint blockade inhibitors. METHODS 10 metastatic TNBC patients received 4 mg TAK-228 and 200 mg TAK-117 (PIKTOR) orally each day for 3 days followed by 4 days off, weekly, until disease progression (PD), followed by intravenous cisplatin 75 mg/m2 plus nab paclitaxel 220 mg/m2 every 3 weeks for up to 6 cycles. Patients received subsequent treatment with pembrolizumab and/or chemotherapy. Primary endpoints were objective response rate with cisplatin/nab paclitaxel and safety. Biopsies of a metastatic lesion were collected prior to and at PD on PIKTOR. Whole exome and RNA-sequencing and reverse phase protein arrays (RPPA) were used to phenotype tumors pre- and post-PIKTOR for alterations in DDR, proliferation, and immune response. RESULTS With cisplatin/nab paclitaxel (cis/nab pac) therapy post PIKTOR, 3 patients had clinical benefit (1 partial response (PR) and 2 stable disease (SD) ≥ 6 months) and continued to have durable benefit in progression-free survival with pembrolizumab post-cis/nab pac for 1.2, 2, and 3.6 years. Their post-PIKTOR metastatic tissue displayed decreased mismatch repair (MMR), increased tumor mutation burden, and significantly lower levels of 53BP1, DAG Lipase β, GCN2, AKT Ser473, and PKCzeta Thr410/403 compared to pre-PIKTOR tumor tissue. CONCLUSIONS Priming patients' chemotherapy-pretreated metastatic TNBC with PIKTOR led to very prolonged response/disease control with subsequent cis/nab pac, followed by pembrolizumab, in 3 of 10 treated patients. Our multi-omics approach revealed a higher number of genomic alterations, reductions in MMR, and alterations in immune and stress response pathways post-PIKTOR in patients who had durable responses. TRIAL REGISTRATION This clinical trial was registered on June 21, 2017, at ClinicalTrials.gov using identifier NCT03193853.
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Affiliation(s)
- Jessica D Lang
- The Translational Genomics Research Institute (TGen), Integrated Cancer Genomics Division, Phoenix, AZ, 85004, USA
- Department of Pathology and Laboratory Medicine, Center for Human Genomics and Precision Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Tuong Vi V Nguyen
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, 22030, USA
| | - Maren K Levin
- Baylor Scott & White Research Institute, Dallas, TX, 75246, USA
| | - Page E Blas
- Baylor Scott & White Research Institute, Dallas, TX, 75246, USA
| | | | | | - Natalia Briones
- The Translational Genomics Research Institute (TGen), Integrated Cancer Genomics Division, Phoenix, AZ, 85004, USA
| | - Claudius Mueller
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, 22030, USA
| | - William Selleck
- The Translational Genomics Research Institute (TGen), Integrated Cancer Genomics Division, Phoenix, AZ, 85004, USA
| | - Sarah Moore
- The Translational Genomics Research Institute (TGen), Integrated Cancer Genomics Division, Phoenix, AZ, 85004, USA
| | - Victoria L Zismann
- The Translational Genomics Research Institute (TGen), Integrated Cancer Genomics Division, Phoenix, AZ, 85004, USA
| | - William P D Hendricks
- The Translational Genomics Research Institute (TGen), Integrated Cancer Genomics Division, Phoenix, AZ, 85004, USA
| | - Virginia Espina
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, 22030, USA
| | - Joyce O'Shaughnessy
- Baylor University Medical Center, Texas Oncology, 3410 Worth Street, Suite 400, Dallas, TX, 75246, USA.
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Reverse Phase Protein Arrays. Methods Mol Biol 2021; 2237:103-122. [PMID: 33237412 DOI: 10.1007/978-1-0716-1064-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Reverse phase protein arrays (RPPA) are used to quantify proteins and protein posttranslational modifications in cellular lysates and body fluids. RPPA technology is suitable for biomarker discovery, protein pathway profiling, functional phenotype analysis, and drug discovery mechanism of action. The principles of RPPA technology are (a) immobilizing protein-containing specimens on a coated slide in discrete spots, (b) antibody recognition of proteins, (c) amplification chemistries to detect the protein-antibody complex, and (d) quantifying spot intensity. Construction of a RPPA begins with the robotic liquid transfer of protein-containing specimens from microtiter plates onto nitrocellulose-coated slides. The robotic arrayer deposits each sample as discrete spots in an array format. Specimens, controls, and calibrators are printed on each array, thus providing a complete calibrated assay on a single slide. Each RPPA slide is subsequently probed with catalyzed signal amplification chemistries and a single primary antibody, a secondary antibody, and either fluorescent or colorimetric dyes. The focus of this chapter is to describe RPPA detection and imaging using a colorimetric (diaminobenzidine (DAB)) detection strategy.
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