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Liao S, Zhou M, Wang Y, Lu C, Yin B, Zhang Y, Liu H, Yin X, Song G. Emerging biomedical imaging-based companion diagnostics for precision medicine. iScience 2023; 26:107277. [PMID: 37520706 PMCID: PMC10371849 DOI: 10.1016/j.isci.2023.107277] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023] Open
Abstract
The tumor heterogeneity, which leads to individual variations in tumor microenvironments, causes poor prognoses and limits therapeutic response. Emerging technology such as companion diagnostics (CDx) detects biomarkers and monitors therapeutic responses, allowing identification of patients who would benefit most from treatment. However, currently, most US Food and Drug Administration-approved CDx tests are designed to detect biomarkers in vitro and ex vivo, making it difficult to dynamically report variations of targets in vivo. Various medical imaging techniques offer dynamic measurement of tumor heterogeneity and treatment response, complementing CDx tests. Imaging-based companion diagnostics allow for patient stratification for targeted medicines and identification of patient populations benefiting from alternative therapeutic methods. This review summarizes recent developments in molecular imaging for predicting and assessing responses to cancer therapies, as well as the various biomarkers used in imaging-based CDx tests. We hope this review provides informative insights into imaging-based companion diagnostics and advances precision medicine.
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Affiliation(s)
- Shiyi Liao
- State Key Laboratory for Chemo, Biosensing and Chemometrics, College of Chemistry and Chemical, Engineering, Hunan University, Changsha 410082, China
| | - Mengjie Zhou
- State Key Laboratory for Chemo, Biosensing and Chemometrics, College of Chemistry and Chemical, Engineering, Hunan University, Changsha 410082, China
| | - Youjuan Wang
- State Key Laboratory for Chemo, Biosensing and Chemometrics, College of Chemistry and Chemical, Engineering, Hunan University, Changsha 410082, China
| | - Chang Lu
- State Key Laboratory for Chemo, Biosensing and Chemometrics, College of Chemistry and Chemical, Engineering, Hunan University, Changsha 410082, China
| | - Baoli Yin
- State Key Laboratory for Chemo, Biosensing and Chemometrics, College of Chemistry and Chemical, Engineering, Hunan University, Changsha 410082, China
| | - Ying Zhang
- State Key Laboratory for Chemo, Biosensing and Chemometrics, College of Chemistry and Chemical, Engineering, Hunan University, Changsha 410082, China
| | - Huiyi Liu
- State Key Laboratory for Chemo, Biosensing and Chemometrics, College of Chemistry and Chemical, Engineering, Hunan University, Changsha 410082, China
| | - Xia Yin
- State Key Laboratory for Chemo, Biosensing and Chemometrics, College of Chemistry and Chemical, Engineering, Hunan University, Changsha 410082, China
| | - Guosheng Song
- State Key Laboratory for Chemo, Biosensing and Chemometrics, College of Chemistry and Chemical, Engineering, Hunan University, Changsha 410082, China
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The diagnostic importance of pathogenic variants and variant coexistence determined by NGS-based liquid biopsy approach in patients with lung adenocarcinoma. Mol Cell Probes 2022; 64:101819. [DOI: 10.1016/j.mcp.2022.101819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/22/2022] [Accepted: 04/22/2022] [Indexed: 11/23/2022]
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Salah HT, DiNardo CD, Konopleva M, Khoury JD. Potential Biomarkers for Treatment Response to the BCL-2 Inhibitor Venetoclax: State of the Art and Future Directions. Cancers (Basel) 2021; 13:2974. [PMID: 34198580 PMCID: PMC8231978 DOI: 10.3390/cancers13122974] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 12/30/2022] Open
Abstract
Intrinsic apoptotic pathway dysregulation plays an essential role in all cancers, particularly hematologic malignancies. This role has led to the development of multiple therapeutic agents targeting this pathway. Venetoclax is a selective BCL-2 inhibitor that has been approved for the treatment of chronic lymphoid leukemia and acute myeloid leukemia. Given the reported resistance to venetoclax, understanding the mechanisms of resistance and the potential biomarkers of response is crucial to ensure optimal drug usage and improved patient outcomes. Mechanisms of resistance to venetoclax include alterations involving the BH3-binding groove, BCL2 gene mutations affecting venetoclax binding, and activation of alternative anti-apoptotic pathways. Moreover, various potential genetic biomarkers of venetoclax resistance have been proposed, including chromosome 17p deletion, trisomy 12, and TP53 loss or mutation. This manuscript provides an overview of biomarkers that could predict treatment response to venetoclax.
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Affiliation(s)
- Haneen T. Salah
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia;
| | - Courtney D. DiNardo
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (C.D.D.); (M.K.)
| | - Marina Konopleva
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (C.D.D.); (M.K.)
| | - Joseph D. Khoury
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Liquid Biopsy by Next-Generation Sequencing: a Multimodality Test for Management of Cancer. Curr Hematol Malig Rep 2020; 14:358-367. [PMID: 31346903 DOI: 10.1007/s11899-019-00532-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE OF REVIEW While liquid biopsy is still relatively a new concept, the advent of next-generation sequencing (NGS) technologies has recently generated a revolution in the field and will be the focus of this review. RECENT FINDINGS Circulating tumor DNA (ctDNA) derives from tumor cells and provides information about the genetic alterations of tumors. However, ctDNA concentration in plasma can be below the level of detection by conventional methods; therefore, screening for actionable genetic information is challenging. Clinical trials exploring targeted and untargeted sequencing to improve the outcomes of ctDNA detection are showing promising results, having reached a limit of detection as low as 0.001% of ctDNA in a background of normal circulating DNA. Most of the challenges related to the sensitivity of detection of ctDNA have been defeated by dint of NGS-based approaches. Despite all the efforts, these methods are still expensive, time-consuming, and require advanced skills for appropriate interpretation. Nevertheless, the technology is rapidly improving, and the expectations for the implementation of liquid biopsy into the clinical practice in the near future are high.
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Sanz-De Pedro M, Wang W, Kanagal-Shamanna R, Khoury JD. Myelodysplastic Syndromes: Laboratory Workup in the Context of New Concepts and Classification Criteria. Curr Hematol Malig Rep 2019; 13:467-476. [PMID: 30338456 DOI: 10.1007/s11899-018-0483-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
PURPOSE OF REVIEW This review provides a comprehensive update of myelodysplastic syndromes (MDS) and their diagnostic criteria, with emphasis on novel concepts and state-of-the-art laboratory workup, including multiparameter/multicolor flow cytometry, chromosome analysis, and mutation profiling. RECENT FINDINGS Recent advances in genetics and molecular technologies have provided unprecedented insights into the pathogenic mechanisms and genomic landscape of MDS and its precursor lesions. This has resulted in revised diagnostic criteria in the World Health Organization (WHO) classification and proposed new terminology for early lesions such as clonal hematopoiesis of indeterminate potential (CHIP). Against this landscape, a thorough understanding of the advantages and limitations of laboratory tests employed in the evaluation of patients with cytopenia has gained unprecedented importance. Healthcare providers involved in the care of patients with hematologic diseases should be aware of the intricacies of laboratory workup of such patients, particularly in view of the novel concepts and classification criteria of MDS.
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Affiliation(s)
- Maria Sanz-De Pedro
- Department of Laboratory Medicine, La Paz University Hospital, Madrid, Spain
| | - Wei Wang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, MS-072, Houston, TX, 77030, USA
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, MS-072, Houston, TX, 77030, USA
| | - Joseph D Khoury
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, MS-072, Houston, TX, 77030, USA.
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Sanchez A, Bocklage T. Precision cytopathology: expanding opportunities for biomarker testing in cytopathology. J Am Soc Cytopathol 2019; 8:95-115. [PMID: 31287426 DOI: 10.1016/j.jasc.2018.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 12/14/2018] [Accepted: 12/15/2018] [Indexed: 06/09/2023]
Abstract
Precision cytopathology refers to therapeutically linked biomarker testing in cytopatology, a dynamically growing area of the discipline. This review describes basic steps to expand precision cytopathology services. Focusing exclusively on solid tumors, the review is divided into four sections: Section 1: Overview of precision pathology- opportunities and challenges; Section 2: Basic steps in establishing or expanding a precision cytopathology laboratory; Section 3: Cytopathology specimens suitable for next generation sequencing platforms; and Section 4: Summary. precision cytopathology continues to rapidly evolve in parallel with expanding targeted therapy options. Biomarker assays (companion diagnostics) comprise a multitude of test types including immunohistochemistry, in situ hybridization and molecular genetic tests such as PCR and next generation sequencing all of which are performable on cytology specimens. Best practices for precision cytopathology will incorporate traditional diagnostic approaches allied with careful specimen triage to enable successful biomarker analysis. Beyond triaging, cytopathologists knowledgeable about molecular test options and capabilities have the opportunity to refine diagnoses, prognoses and predictive information thereby assuming a lead role in precision oncology biomarker testing.
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Affiliation(s)
| | - Thèrése Bocklage
- Department of Pathology and Laboratory Medicine, University of Kentucky College of Medicine, MS.
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Khoury JD, Wang WL, Prieto VG, Medeiros LJ, Kalhor N, Hameed M, Broaddus R, Hamilton SR. Validation of Immunohistochemical Assays for Integral Biomarkers in the NCI-MATCH EAY131 Clinical Trial. Clin Cancer Res 2017; 24:521-531. [PMID: 28839110 DOI: 10.1158/1078-0432.ccr-17-1597] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 07/06/2017] [Accepted: 08/09/2017] [Indexed: 12/21/2022]
Abstract
Biomarkers that guide therapy selection are gaining unprecedented importance as targeted therapy options increase in scope and complexity. In conjunction with high-throughput molecular techniques, therapy-guiding biomarker assays based upon immunohistochemistry (IHC) have a critical role in cancer care in that they inform about the expression status of a protein target. Here, we describe the validation procedures for four clinical IHC biomarker assays-PTEN, RB, MLH1, and MSH2-for use as integral biomarkers in the nationwide NCI-Molecular Analysis for Therapy Choice (NCI-MATCH) EAY131 clinical trial. Validation procedures were developed through an iterative process based on collective experience and adaptation of broad guidelines from the FDA. The steps included primary antibody selection; assay optimization; development of assay interpretation criteria incorporating biological considerations; and expected staining patterns, including indeterminate results, orthogonal validation, and tissue validation. Following assay lockdown, patient samples and cell lines were used for analytic and clinical validation. The assays were then approved as laboratory-developed tests and used for clinical trial decisions for treatment selection. Calculations of sensitivity and specificity were undertaken using various definitions of gold-standard references, and external validation was required for the PTEN IHC assay. In conclusion, validation of IHC biomarker assays critical for guiding therapy in clinical trials is feasible using comprehensive preanalytic, analytic, and postanalytic steps. Implementation of standardized guidelines provides a useful framework for validating IHC biomarker assays that allow for reproducibility across institutions for routine clinical use. Clin Cancer Res; 24(3); 521-31. ©2017 AACR.
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Affiliation(s)
- Joseph D Khoury
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Wei-Lien Wang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Victor G Prieto
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Neda Kalhor
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Russell Broaddus
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stanley R Hamilton
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Stricker RB, Johnson L. Lyme disease: the promise of Big Data, companion diagnostics and precision medicine. Infect Drug Resist 2016; 9:215-9. [PMID: 27672336 PMCID: PMC5024771 DOI: 10.2147/idr.s114770] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Lyme disease caused by the spirochete Borrelia burgdorferi has become a major worldwide epidemic. Recent studies based on Big Data registries show that >300,000 people are diagnosed with Lyme disease each year in the USA, and up to two-thirds of individuals infected with B. burgdorferi will fail conventional 30-year-old antibiotic therapy for Lyme disease. In addition, animal and human evidence suggests that sexual transmission of the Lyme spirochete may occur. Improved companion diagnostic tests for Lyme disease need to be implemented, and novel treatment approaches are urgently needed to combat the epidemic. In particular, therapies based on the principles of precision medicine could be modeled on successful "designer drug" treatment for HIV/AIDS and hepatitis C virus infection featuring targeted protease inhibitors. The use of Big Data registries, companion diagnostics and precision medicine will revolutionize the diagnosis and treatment of Lyme disease.
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