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An analysis of research biopsy core variability from over 5000 prospectively collected core samples. NPJ Precis Oncol 2021; 5:94. [PMID: 34707215 PMCID: PMC8551285 DOI: 10.1038/s41698-021-00234-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 09/22/2021] [Indexed: 12/28/2022] Open
Abstract
Factors correlated with biopsy tissue adequacy and the prevalence of within-biopsy variability were evaluated. Totally, 1149 research biopsies were performed on 686 patients from which 5090 cores were assessed. Biopsy cores were reviewed for malignant percentage (estimated percentage of cells in the core that were malignant) and malignant area (estimated area occupied by malignant cells). Linear mixed models and generalized linear mixed models were used for the analysis. A total of 641 (55.8%) biopsies contained a core with <10% malignant percentage (inadequate core). The chance of an inadequate core was not influenced by core order, though the malignant area decreased with each consecutive core (p < 0.001). Younger age, bone biopsy location, appendiceal tumor pathology, and responding/stable disease prior to biopsy increased the odds of a biopsy containing zero adequate cores. Within-biopsy variability in core adequacy is prevalent and suggests the need for histological tumor quality assessment of each core in order to optimize translational analyses.
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2
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Lazcano R, Rojas F, Laberiano C, Hernandez S, Parra ER. Pathology Quality Control for Multiplex Immunofluorescence and Image Analysis Assessment in Longitudinal Studies. Front Mol Biosci 2021; 8:661222. [PMID: 34395517 PMCID: PMC8363080 DOI: 10.3389/fmolb.2021.661222] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 07/19/2021] [Indexed: 11/28/2022] Open
Abstract
Immune profiling of formalin-fixed, paraffin-embedded tissues using multiplex immunofluorescence (mIF) staining and image analysis methodology allows for the study of several biomarkers on a single slide. The pathology quality control (PQC) for tumor tissue immune profiling using digital image analysis of core needle biopsies is an important step in any laboratory to avoid wasting time and materials. Although there are currently no established inclusion and exclusion criteria for samples used in this type of assay, a PQC is necessary to achieve accurate and reproducible data. We retrospectively reviewed PQC data from hematoxylin and eosin (H&E) slides and from mIF image analysis samples obtained during 2019. We reviewed a total of 931 reports from core needle biopsy samples; 123 (13.21%) were excluded during the mIF PQC. The most common causes of exclusion were the absence of malignant cells or fewer than 100 malignant cells in the entire section (n = 42, 34.15%), tissue size smaller than 4 × 1 mm (n = 16, 13.01%), fibrotic tissue without inflammatory cells (n = 12, 9.76%), and necrotic tissue (n = 11, 8.94%). Baseline excluded samples had more fibrosis (90 vs 10%) and less necrosis (5 vs 90%) compared with post-treatment excluded samples. The most common excluded organ site of the biopsy was the liver (n = 19, 15.45%), followed by soft tissue (n = 17, 13.82%) and the abdominal region (n = 15, 12.20%). We showed that the PQC is an important step for image analysis and that the absence of malignant cells is the most limiting sample characteristic for mIF image analysis. We also discuss other challenges that pathologists need to consider to report reliable and reproducible image analysis data.
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Affiliation(s)
| | | | | | | | - Edwin Roger Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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3
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Xu M, Tapia C, Hajjar J, Sabir S, Colen R, Nagarajan P, Aung PP, Gong J, Rodon J, Fu S, Stephen B, Roy-Chowdhuri S, Le H, Yang V, Zarifa A, Abdelsalam ME, Jhingran A, Javle M, Pant S, Carter B, Milton DR, Sun R, Karp DD, Koay EJ, Yang Y, Wistuba II, Hwu P, Meric-Bernstam F, Naing A. Implementation of a Novel Web-Based Lesion Selection Tool to Improve Acquisition of Tumor Biopsy Specimens. JOURNAL OF IMMUNOTHERAPY AND PRECISION ONCOLOGY 2021; 4:45-52. [PMID: 35663531 DOI: 10.36401/jipo-21-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/14/2021] [Accepted: 03/17/2021] [Indexed: 12/17/2022]
Abstract
Introduction For maximum utility of molecular characterization by next-generation sequencing (NGS) and better understanding of tumor microenvironment with immune correlates analysis, biopsy specimens must yield adequate tumor tissue, and sequential biopsy specimens should sample a consistent site. We developed a web-based lesion selection tool (LST) that enables management and tracking of the biopsy specimen collections. Methods Of 145 patients, the LST was used for 88 patients; the other 57 served as controls. We evaluated consistency of the lesion biopsied in longitudinal collections, number of cores obtained, and cores with adequate tumor cellularity for NGS. The Fisher exact test and Wilcoxon rank sum test were used to identify differences between the groups. Results The analysis included 30 of 88 (34%) patients in the LST group and 52 of 57 (91%) in the control group. The LST workflow ensured 100% consistency in the lesions biopsied compared with 75% in the control group in longitudinal collections and increased the proportion of patients in whom at least five cores were collected per biopsy. Conclusions The novel LST platform facilitates coordination, performance, and management of longitudinal biopsy specimens. Use of the LST enables sampling of the designated lesion consistently, which is likely to accurately inform us the effect of the treatment on tumor microenvironment and evolution of resistant pathways. Such studies are important translational component of any clinical trials and research as they guide the development of next line of therapy, which has significant effect on clinical utility. However, validation of this approach in a larger study is warranted.
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Affiliation(s)
- Mingxuan Xu
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Coya Tapia
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joud Hajjar
- Section of Immunology, Allergy and Rheumatology, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Sharjeel Sabir
- Department of Interventional Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rivka Colen
- Department of Diagnostic Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Priyadharsini Nagarajan
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Phyu P Aung
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jing Gong
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jordi Rodon
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Siqing Fu
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bettzy Stephen
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sinchita Roy-Chowdhuri
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hung Le
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vincent Yang
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Abdulrazzak Zarifa
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mohamed Elsayed Abdelsalam
- Department of Interventional Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anuja Jhingran
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Milind Javle
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shubham Pant
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Brett Carter
- Section of Thoracic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Denai R Milton
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ryan Sun
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Daniel D Karp
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Eugene Jon Koay
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yali Yang
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Patrick Hwu
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Aung Naing
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Herrick WG, Kilpatrick CL, Hollingshead MG, Esposito D, O'Sullivan Coyne G, Gross AM, Johnson BC, Chen AP, Widemann BC, Doroshow JH, Parchment RE, Srivastava AK. Isoform- and Phosphorylation-specific Multiplexed Quantitative Pharmacodynamics of Drugs Targeting PI3K and MAPK Signaling in Xenograft Models and Clinical Biopsies. Mol Cancer Ther 2021; 20:749-760. [PMID: 33536190 PMCID: PMC8026683 DOI: 10.1158/1535-7163.mct-20-0566] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/16/2020] [Accepted: 02/01/2021] [Indexed: 11/16/2022]
Abstract
Ras/Raf/MEK/ERK (MAPK) and PI3K/AKT signaling pathways influence several cell functions involved in oncogenesis, making them attractive drug targets. We describe a novel multiplex immunoassay to quantitate isoform-specific phosphorylation of proteins in the PI3K/AKT and MAPK pathways as a tool to assess pharmacodynamic changes. Isoform-specific assays measuring total protein and site-specific phosphorylation levels of ERK1/2, MEK1/2, AKT1/2/3, and rpS6 were developed on the Luminex platform with validated antibody reagents. The multiplex assay demonstrated satisfactory analytic performance. Fit-for-purpose validation was performed with xenograft models treated with selected agents. In PC3 and HCC70 xenograft tumors, the PI3Kβ inhibitor AZD8186 suppressed phosphorylation of AKT1, AKT2, and rpS6 for 4 to 7 hours post single dose, but levels returned to baseline by 24 hours. AKT3 phosphorylation was suppressed in PC3 xenografts at all doses tested, but only at the highest dose in HCC70. The AKT inhibitor MK-2206 reduced AKT1/2/3 phosphorylation in SW620 xenograft tumors 2 to 4 hours postdose, and the MEK inhibitor selumetinib reduced MEK1/2 and ERK1/2 phosphorylation by up to 50% and >90%, respectively. Clinical utility was demonstrated by analyzing biopsies from untreated patients with plexiform neurofibromas enrolled in a clinical trial of selumetinib (NCT02407405). These biopsies showed MEK and ERK phosphorylation levels sufficient for measuring up to 90% inhibition, and low AKT and rpS6 phosphorylation. This validated multiplex immunoassay demonstrates the degree and duration of phosphorylation modulation for three distinct classes of drugs targeting the PI3K/AKT and MAPK pathways.
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Affiliation(s)
- William G Herrick
- Clinical Pharmacodynamics Biomarker Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Casey L Kilpatrick
- Clinical Pharmacodynamics Biomarker Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | | | - Dominic Esposito
- Protein Expression Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | | | - Andrea M Gross
- Pediatric Oncology Branch, NCI, Bethesda, Maryland
- Center for Cancer Research, NCI, Bethesda, Maryland
| | - Barry C Johnson
- Division of Cancer Treatment and Diagnosis, NCI, Bethesda, Maryland
| | - Alice P Chen
- Division of Cancer Treatment and Diagnosis, NCI, Bethesda, Maryland
| | - Brigitte C Widemann
- Pediatric Oncology Branch, NCI, Bethesda, Maryland
- Center for Cancer Research, NCI, Bethesda, Maryland
| | - James H Doroshow
- Division of Cancer Treatment and Diagnosis, NCI, Bethesda, Maryland
- Center for Cancer Research, NCI, Bethesda, Maryland
| | - Ralph E Parchment
- Clinical Pharmacodynamics Biomarker Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Apurva K Srivastava
- Clinical Pharmacodynamics Biomarker Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland.
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Hu-Lieskovan S, Bhaumik S, Dhodapkar K, Grivel JCJB, Gupta S, Hanks BA, Janetzki S, Kleen TO, Koguchi Y, Lund AW, Maccalli C, Mahnke YD, Novosiadly RD, Selvan SR, Sims T, Zhao Y, Maecker HT. SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery. J Immunother Cancer 2020; 8:e000705. [PMID: 33268350 PMCID: PMC7713206 DOI: 10.1136/jitc-2020-000705] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2020] [Indexed: 02/07/2023] Open
Abstract
Since the publication of the Society for Immunotherapy of Cancer's (SITC) original cancer immunotherapy biomarkers resource document, there have been remarkable breakthroughs in cancer immunotherapy, in particular the development and approval of immune checkpoint inhibitors, engineered cellular therapies, and tumor vaccines to unleash antitumor immune activity. The most notable feature of these breakthroughs is the achievement of durable clinical responses in some patients, enabling long-term survival. These durable responses have been noted in tumor types that were not previously considered immunotherapy-sensitive, suggesting that all patients with cancer may have the potential to benefit from immunotherapy. However, a persistent challenge in the field is the fact that only a minority of patients respond to immunotherapy, especially those therapies that rely on endogenous immune activation such as checkpoint inhibitors and vaccination due to the complex and heterogeneous immune escape mechanisms which can develop in each patient. Therefore, the development of robust biomarkers for each immunotherapy strategy, enabling rational patient selection and the design of precise combination therapies, is key for the continued success and improvement of immunotherapy. In this document, we summarize and update established biomarkers, guidelines, and regulatory considerations for clinical immune biomarker development, discuss well-known and novel technologies for biomarker discovery and validation, and provide tools and resources that can be used by the biomarker research community to facilitate the continued development of immuno-oncology and aid in the goal of durable responses in all patients.
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Affiliation(s)
- Siwen Hu-Lieskovan
- Huntsman Cancer Institute, Salt Lake City, UT, USA
- University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Kavita Dhodapkar
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | | | - Sumati Gupta
- Huntsman Cancer Institute, Salt Lake City, Utah, USA
| | - Brent A Hanks
- Duke University Medical Center, Durham, North Carolina, USA
| | | | | | - Yoshinobu Koguchi
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
| | - Amanda W Lund
- Oregon Health and Science University, Portland, Oregon, USA
| | | | | | | | | | - Tasha Sims
- Regeneron Pharmaceuticals Inc, Tarrytown, New York, USA
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6
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Krishnamurthy S, Sabir S, Ban K, Wu Y, Sheth R, Tam A, Meric-Bernstam F, Shaw K, Mills G, Bassett R, Hamilton S, Hicks M, Gupta S. Comparison of Real-Time Fluorescence Confocal Digital Microscopy With Hematoxylin-Eosin-Stained Sections of Core-Needle Biopsy Specimens. JAMA Netw Open 2020; 3:e200476. [PMID: 32134465 PMCID: PMC7059022 DOI: 10.1001/jamanetworkopen.2020.0476] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
IMPORTANCE Strategies to procure high-quality core-needle biopsy (CNB) specimens are critical for making basic tissue diagnoses and for ancillary testing. OBJECTIVES To investigate acquisition of fluorescence confocal microscopy (FCM) images of interventional radiology (IR)-guided CNB in real time in the radiology suite and to compare the accuracy of FCM diagnoses with those of hematoxylin-eosin (H&E)-stained CNB sections. DESIGN, SETTING, AND PARTICIPANTS In this diagnostic study, FCM imaging of IR-guided CNBs was performed in the radiology suite at a major cancer center for patients with an imaging abnormality from August 1, 2016, to April 30, 2019. The time taken to acquire FCM images and the quality of FCM images based on percentage of interpretable tissue with optimal resolution was recorded. The FCM images were read by 2 pathologists and categorized as nondiagnostic, benign/atypical, or suspicious/malignant; these diagnoses were compared with those made using H&E-stained tissue sections. Cases with discrepant diagnosis were reassessed by the pathologists together for a consensus diagnosis. Data were analyzed from June 3 to July 19, 2019. INTERVENTIONS Each IR-guided CNB was stained with 0.6mM acridine orange, subjected to FCM imaging, and then processed to generate H&E-stained sections. MAIN OUTCOMES AND MEASURES Mean time taken for acquisition of FCM images, quality of FCM images based on interpretable percentage of the image, and accuracy of diagnostic categorization based on FCM images compared with H&E-stained sections. RESULTS A total of 105 patients (57 male [54.3%]; mean [SD] age, 63 [13] years) underwent IR-guided CNBs in a mean (SD) of 7 (2) minutes each. The FCM images showed at least 20% of the tissue with optimal quality in 101 CNB specimens (96.2%). The FCM images were accurately interpreted by the 2 pathologists in 100 of 105 cases (95.2%) (2 false-positive and 3 false-negative) and 90 of 105 cases (85.7%) (6 false-positive and 9 false-negative). A reassessment of 14 discordant diagnoses resulted in consensus diagnoses that were accurate in 101 of 105 cases (96.2%) (1 false-positive and 3 false-negative). CONCLUSIONS AND RELEVANCE The ease of acquisition of FCM images of acceptable quality and the high accuracy of the diagnoses suggest that FCM may be useful for rapid evaluation of IR-guided CNBs. This approach warrants further investigation.
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Affiliation(s)
- Savitri Krishnamurthy
- Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston
| | - Sharjeel Sabir
- Department of Radiology, Scripps Mercy Hospital, San Diego, California
| | - Kechen Ban
- Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston
| | - Yun Wu
- Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston
| | - Rahul Sheth
- Department of Interventional Radiology, The University of Texas MD Anderson Cancer Center, Houston
| | - Alda Tam
- Department of Interventional Radiology, The University of Texas MD Anderson Cancer Center, Houston
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston
| | - Kenna Shaw
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston
| | - Gordon Mills
- Oregon Health and Science University Knight Cancer Institute, Portland
| | - Roland Bassett
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston
| | - Stanley Hamilton
- Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston
| | - Marshall Hicks
- Department of Interventional Radiology, The University of Texas MD Anderson Cancer Center, Houston
| | - Sanjay Gupta
- Department of Interventional Radiology, The University of Texas MD Anderson Cancer Center, Houston
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7
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Lara OD, Krishnan S, Wang Z, Corvigno S, Zhong Y, Lyons Y, Dood R, Hu W, Qi L, Liu J, Coleman RL, Westin SN, Fleming ND, Cristini V, Rao A, Burks J, Sood AK. Tumor core biopsies adequately represent immune microenvironment of high-grade serous carcinoma. Sci Rep 2019; 9:17589. [PMID: 31772388 PMCID: PMC6879510 DOI: 10.1038/s41598-019-53872-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 10/18/2019] [Indexed: 11/22/2022] Open
Abstract
The prognostic and therapeutic value of the tumor microenvironment (TME) in various cancer types is of major interest. Characterization of the TME often relies on a small representative tissue sample. However, the adequacy of such a sample for assessing components of the TME is not yet known. Here, we used immunohistochemical (IHC) staining and 7-color multiplex staining to evaluate CD8 (cluster of differentiation 8), CD68, PD-L1 (programmed death-ligand 1), CD34, FAP (fibroblast activation protein), and cytokeratin in 220 tissue cores from 26 high-grade serous ovarian cancer samples. Comparisons were drawn between a larger tumor specimen and smaller core biopsies based on number and location (central tumor vs. peripheral tumor) of biopsies. Our analysis found that the correlation between marker-specific cell subsets in larger tumor versus smaller core was stronger with two core biopsies and was not further strengthened with additional biopsies. Moreover, this correlation was consistently strong regardless of whether the biopsy was taken at the center or at the periphery of the original tumor sample. These findings could have a substantial impact on longitudinal assessment for detection of biomarkers in clinical trials.
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Affiliation(s)
- Olivia D Lara
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Santhoshi Krishnan
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, 77030, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Zhihui Wang
- Mathematics in Medicine Program, Houston Methodist Research Institute, Houston, TX, 77030, USA
| | - Sara Corvigno
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - YanPing Zhong
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Department of Pathology, The First Hospital of Jilin University, Changchun, China
| | - Yasmin Lyons
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Robert Dood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Wei Hu
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Lisha Qi
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jinsong Liu
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Robert L Coleman
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Shannon N Westin
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Nicole D Fleming
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Vittorio Cristini
- Mathematics in Medicine Program, Houston Methodist Research Institute, Houston, TX, 77030, USA.,Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Arvind Rao
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, 77030, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jared Burks
- Flow Cytometry and Cell Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Anil K Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. .,Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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8
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Ferry-Galow KV, Chen AP. The use of research biopsies in oncology trials: challenges and controversies. JOURNAL OF HOSPITAL MANAGEMENT AND HEALTH POLICY 2019; 3:7. [PMID: 31187090 PMCID: PMC6557427 DOI: 10.21037/jhmhp.2019.03.01] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Katherine V. Ferry-Galow
- Clinical Pharmacodynamic Program, Applied/Developmental
Research Directorate, Leidos Biomedical Research, Inc., Frederick National
Laboratory for Cancer Research, Frederick, MD, USA
| | - Alice P. Chen
- Early Clinical Trials Development Program, Division of
Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, USA
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9
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Ferry-Galow KV, Datta V, Makhlouf HR, Wright J, Wood BJ, Levy E, Pisano ED, Tam AL, Lee SI, Mahmood U, Rubinstein LV, Doroshow JH, Chen AP. What Can Be Done to Improve Research Biopsy Quality in Oncology Clinical Trials? J Oncol Pract 2018; 14:JOP1800092. [PMID: 30285529 PMCID: PMC6237512 DOI: 10.1200/jop.18.00092] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
PURPOSE: Research biopsy specimens collected in clinical trials often present requirements beyond those of tumor biopsy specimens collected for diagnostic purposes. Research biopsies underpin hypothesis-driven drug development, pharmacodynamic assessment of molecularly targeted anticancer agents, and, increasingly, genomic assessment for precision medicine; insufficient biopsy specimen quality or quantity therefore compromises the scientific value of a study and the resources devoted to it, as well as each patient's contribution to and potential benefit from a clinical trial. METHODS: To improve research biopsy specimen quality, we consulted with other translational oncology teams and reviewed current best practices. RESULTS: Among the recommendations were improving communication between oncologists and interventional radiologists, providing feedback on specimen sufficiency, increasing academic recognition and financial support for the time investment required by radiologists to collect and preserve research biopsy specimens, and improving real-time assessment of tissue quality. CONCLUSION: Implementing these recommendations at the National Cancer Institute's Developmental Therapeutics Clinic has demonstrably improved the quality of biopsy specimens collected; more widespread dissemination of these recommendations beyond large clinical cancer centers is possible and will be of value to the community in improving clinical research and, ultimately, patient care.
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Affiliation(s)
- Katherine V. Ferry-Galow
- Frederick National Laboratory for Cancer Research, Frederick; National Cancer Institute, Bethesda MD; Beth Israel Deaconess Medical Center; Harvard Medical School; Massachusetts General Hospital, Boston, MA; American College of Radiology, Reston, VA; and University of Texas MD Anderson Cancer Center, Houston, TX
| | - Vivekananda Datta
- Frederick National Laboratory for Cancer Research, Frederick; National Cancer Institute, Bethesda MD; Beth Israel Deaconess Medical Center; Harvard Medical School; Massachusetts General Hospital, Boston, MA; American College of Radiology, Reston, VA; and University of Texas MD Anderson Cancer Center, Houston, TX
| | - Hala R. Makhlouf
- Frederick National Laboratory for Cancer Research, Frederick; National Cancer Institute, Bethesda MD; Beth Israel Deaconess Medical Center; Harvard Medical School; Massachusetts General Hospital, Boston, MA; American College of Radiology, Reston, VA; and University of Texas MD Anderson Cancer Center, Houston, TX
| | - John Wright
- Frederick National Laboratory for Cancer Research, Frederick; National Cancer Institute, Bethesda MD; Beth Israel Deaconess Medical Center; Harvard Medical School; Massachusetts General Hospital, Boston, MA; American College of Radiology, Reston, VA; and University of Texas MD Anderson Cancer Center, Houston, TX
| | - Bradford J. Wood
- Frederick National Laboratory for Cancer Research, Frederick; National Cancer Institute, Bethesda MD; Beth Israel Deaconess Medical Center; Harvard Medical School; Massachusetts General Hospital, Boston, MA; American College of Radiology, Reston, VA; and University of Texas MD Anderson Cancer Center, Houston, TX
| | - Elliot Levy
- Frederick National Laboratory for Cancer Research, Frederick; National Cancer Institute, Bethesda MD; Beth Israel Deaconess Medical Center; Harvard Medical School; Massachusetts General Hospital, Boston, MA; American College of Radiology, Reston, VA; and University of Texas MD Anderson Cancer Center, Houston, TX
| | - Etta D. Pisano
- Frederick National Laboratory for Cancer Research, Frederick; National Cancer Institute, Bethesda MD; Beth Israel Deaconess Medical Center; Harvard Medical School; Massachusetts General Hospital, Boston, MA; American College of Radiology, Reston, VA; and University of Texas MD Anderson Cancer Center, Houston, TX
| | - Alda L. Tam
- Frederick National Laboratory for Cancer Research, Frederick; National Cancer Institute, Bethesda MD; Beth Israel Deaconess Medical Center; Harvard Medical School; Massachusetts General Hospital, Boston, MA; American College of Radiology, Reston, VA; and University of Texas MD Anderson Cancer Center, Houston, TX
| | - Susanna I. Lee
- Frederick National Laboratory for Cancer Research, Frederick; National Cancer Institute, Bethesda MD; Beth Israel Deaconess Medical Center; Harvard Medical School; Massachusetts General Hospital, Boston, MA; American College of Radiology, Reston, VA; and University of Texas MD Anderson Cancer Center, Houston, TX
| | - Umar Mahmood
- Frederick National Laboratory for Cancer Research, Frederick; National Cancer Institute, Bethesda MD; Beth Israel Deaconess Medical Center; Harvard Medical School; Massachusetts General Hospital, Boston, MA; American College of Radiology, Reston, VA; and University of Texas MD Anderson Cancer Center, Houston, TX
| | - Lawrence V. Rubinstein
- Frederick National Laboratory for Cancer Research, Frederick; National Cancer Institute, Bethesda MD; Beth Israel Deaconess Medical Center; Harvard Medical School; Massachusetts General Hospital, Boston, MA; American College of Radiology, Reston, VA; and University of Texas MD Anderson Cancer Center, Houston, TX
| | - James H. Doroshow
- Frederick National Laboratory for Cancer Research, Frederick; National Cancer Institute, Bethesda MD; Beth Israel Deaconess Medical Center; Harvard Medical School; Massachusetts General Hospital, Boston, MA; American College of Radiology, Reston, VA; and University of Texas MD Anderson Cancer Center, Houston, TX
| | - Alice P. Chen
- Frederick National Laboratory for Cancer Research, Frederick; National Cancer Institute, Bethesda MD; Beth Israel Deaconess Medical Center; Harvard Medical School; Massachusetts General Hospital, Boston, MA; American College of Radiology, Reston, VA; and University of Texas MD Anderson Cancer Center, Houston, TX
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10
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Srivastava AK, Navas T, Herrick WG, Hollingshead MG, Bottaro DP, Doroshow JH, Parchment RE. Effective implementation of novel MET pharmacodynamic assays in translational studies. ANNALS OF TRANSLATIONAL MEDICINE 2017; 5:3. [PMID: 28164088 DOI: 10.21037/atm.2016.12.78] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
MET tyrosine kinase (TK) dysregulation is significantly implicated in many types of cancer. Despite over 20 years of drug development to target MET in cancers, a pure anti-MET therapeutic has not yet received market approval. The failure of two recently concluded phase III trials point to a major weakness in biomarker strategies to identify patients who will benefit most from MET therapies. The capability to interrogate oncogenic mutations in MET via circulating tumor DNA (ctDNA) provides an important advancement in identification and stratification of patients for MET therapy. However, a wide range in type and frequency of these mutations suggest there is a need to carefully link these mutations to MET dysregulation, at least in proof-of-concept studies. In this review, we elaborate how we can utilize recently developed and validated pharmacodynamic biomarkers of MET not only to show target engagement, but more importantly to quantitatively measure MET dysregulation in tumor tissues. The MET assay endpoints provide evidence of both canonical and non-canonical MET signaling, can be used as "effect markers" to define biologically effective doses (BEDs) for molecularly targeted drugs, confirm mechanism-of-action in testing combination of drugs, and establish whether a diagnostic test is reporting MET dysregulation. We have established standard operating procedures for tumor biopsy collections to control pre-analytical variables that have produced valid results in proof-of-concept studies. The reagents and procedures are made available to the research community for potential implementation on multiple platforms such as ELISA, quantitative immunofluorescence assay (qIFA), and immuno-MRM assays.
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Affiliation(s)
- Apurva K Srivastava
- Laboratory of Human Toxicology and Pharmacology, Applied/Developmental Research Directorate, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Tony Navas
- Laboratory of Human Toxicology and Pharmacology, Applied/Developmental Research Directorate, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - William G Herrick
- Laboratory of Human Toxicology and Pharmacology, Applied/Developmental Research Directorate, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Melinda G Hollingshead
- Biological Testing Branch, Developmental Therapeutics Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Donald P Bottaro
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - James H Doroshow
- Division of Cancer Treatment and Diagnosis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Ralph E Parchment
- Laboratory of Human Toxicology and Pharmacology, Applied/Developmental Research Directorate, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
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