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Michalska-Falkowska A, Niklinski J, Juhl H, Sulewska A, Kisluk J, Charkiewicz R, Ciborowski M, Ramlau R, Gryczka R, Piwkowski C, Kozlowski M, Miskiewicz B, Biecek P, Wnorowska K, Dzieciol-Anikiej Z, Sargsyan K, Naumnik W, Mroz R, Reszec-Gielazyn J. Applied Molecular-Based Quality Control of Biobanked Samples for Multi-Omics Approach. Cancers (Basel) 2023; 15:3742. [PMID: 37509403 PMCID: PMC10378006 DOI: 10.3390/cancers15143742] [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: 06/20/2023] [Revised: 07/16/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Biobanks are vital for high-throughput translational research, but the rapid development of novel molecular techniques, especially in omics assays, poses challenges to traditional practices and recommendations. In our study, we used biospecimens from oncological patients in Polish clinics and collaborated with the Indivumed Group. For serum/plasma samples, we monitored hemolysis, controlled RNA extraction, assessed cDNA library quality and quantity, and verified NGS raw data. Tissue samples underwent pathologic evaluation to confirm histology and determine tumor content. Molecular quality control measures included evaluating the RNA integrity number, assessing cDNA library quality and quantity, and analyzing NGS raw data. Our study yielded the creation of distinct workflows for conducting preanalytical quality control of serum/plasma and fresh-frozen tissue samples. These workflows offer customization options to suit the capabilities of different biobanking entities. In order to ensure the appropriateness of biospecimens for advanced research applications, we introduced molecular-based quality control methods that align with the demands of high-throughput assays. The novelty of proposed workflows, rooted in innovative molecular techniques, lies in the integration of these QC methods into a comprehensive schema specifically designed for high-throughput research applications.
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Affiliation(s)
- Anna Michalska-Falkowska
- Biobank, Medical University of Bialystok, 15-269 Bialystok, Poland
- Indivumed Services, 20251 Hamburg, Germany
| | - Jacek Niklinski
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
| | | | - Anetta Sulewska
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Joanna Kisluk
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Radoslaw Charkiewicz
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland
- Center of Experimental Medicine, Medical University of Bialystok, 15-369 Bialystok, Poland
| | - Michal Ciborowski
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland
| | - Rodryg Ramlau
- Department of Oncology, Poznan University of Medical Sciences, 60-569 Poznan, Poland
| | - Robert Gryczka
- Department of Oncology, Poznan University of Medical Sciences, 60-569 Poznan, Poland
| | - Cezary Piwkowski
- Department of Thoracic Surgery, Poznan University of Medical Sciences, 60-569 Poznan, Poland
| | - Miroslaw Kozlowski
- Department of Thoracic Surgery, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Borys Miskiewicz
- Department of Thoracic Surgery, Medical University of Bialystok, 15-269 Bialystok, Poland
| | - Przemyslaw Biecek
- Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland
| | - Karolina Wnorowska
- Department of Medical Pathomorphology, Medical University of Bialystok, 15-269 Bialystok, Poland
- Department of Paediatrics and Pediatric Neurology, Jedrzej Sniadecki Independent Public Healthcare Centre Regional Hospital, 15-278 Bialystok, Poland
| | - Zofia Dzieciol-Anikiej
- Biobank, Medical University of Bialystok, 15-269 Bialystok, Poland
- Department of Rehabilitation, Medical University of Bialystok, 15-089 Bialystok, Poland
| | - Karine Sargsyan
- International Biobanking and Education, Medical University of Graz, 8036 Graz, Austria
- Cancer Biobank at Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Wojciech Naumnik
- 1st Department of Lung Diseases and Tuberculosis, Medical University of Bialystok, 15-540 Bialystok, Poland
| | - Robert Mroz
- 2nd Department of Lung Diseases and Tuberculosis, Medical University of Bialystok, 15-540 Bialystok, Poland
| | - Joanna Reszec-Gielazyn
- Biobank, Medical University of Bialystok, 15-269 Bialystok, Poland
- Department of Medical Pathomorphology, Medical University of Bialystok, 15-269 Bialystok, Poland
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2
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Wiseman EJ, Moss JI, Atkinson J, Baakza H, Hayes E, Willis SE, Waring PM, Rodriguez Canales J, Jones GN. Epitope Lability of Phosphorylated Biomarkers of the DNA Damage Response Pathway Results in Increased Vulnerability to Effects of Delayed or Incomplete Formalin Fixation. J Histochem Cytochem 2023; 71:237-257. [PMID: 37119278 PMCID: PMC10227880 DOI: 10.1369/00221554231174069] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/09/2023] [Indexed: 05/01/2023] Open
Abstract
Phosphorylated biomarkers are crucial for our understanding of drug mechanism of action and dose selection during clinical trials, particularly for drugs that target protein kinases, such as DNA-damage-response (DDR) inhibitors. However, tissue fixation conditions needed to preserve DDR-specific phospho-biomarkers have not been previously investigated. Using xenograft tissues and tightly controlled formalin fixation conditions, we assessed how preanalytical factors affect phosphorylated DDR biomarkers pRAD50(Ser635), ɣH2AX(Ser139), pKAP1(Ser824), and non-phosphorylated biomarkers cMYC and ATM. Cold ischemia times ranged from 15 min to 6 hr, and the fixation duration ranged from 24 hr to 4 weeks. Epitopes pRAD50 and pKAP1 appeared the most labile assessed with staining loss after just 15 min of cold ischemia time, while ATM was more robust showing consistent expression up to 1 hr of cold ischemia. Notably, ɣH2AX expression was lost with formalin fixation over 48 hr. The use of core needle biopsies where possible and novel fixation methods such as the 2-step temperature-controlled formalin approach may improve phosphorylated biomarker preservation; however, practical challenges may affect wider clinical application. The most essential tissue-processing step when downstream analysis includes DDR phosphorylated biomarkers is immediate tissue submersion in formalin, without delay, upon excision from the patient, followed by room temperature fixation for 24 hr.
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Affiliation(s)
| | - Jennifer I. Moss
- Bioscience, Oncology R&D, AstraZeneca,
Cambridge, United Kingdom
| | - James Atkinson
- CPSS, Oncology R&D, AstraZeneca, Cambridge,
United Kingdom
| | - Hana Baakza
- Translational Medicine, Oncology R&D,
AstraZeneca, Cambridge, United Kingdom
| | - Emily Hayes
- Translational Medicine, Oncology R&D,
AstraZeneca, Cambridge, United Kingdom
| | - Sophie E. Willis
- Translational Medicine, Oncology R&D,
AstraZeneca, Cambridge, United Kingdom
| | - Paul M. Waring
- Translational Medicine, Oncology R&D,
AstraZeneca, Cambridge, United Kingdom
| | | | - Gemma N. Jones
- Translational Medicine, Oncology R&D,
AstraZeneca, Cambridge, United Kingdom
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3
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Shutova MS, Borowczyk J, Russo B, Sellami S, Drukala J, Wolnicki M, Brembilla NC, Kaya G, Ivanov AI, Boehncke WH. Inflammation modulates intercellular adhesion and mechanotransduction in human epidermis via ROCK2. iScience 2023; 26:106195. [PMID: 36890793 PMCID: PMC9986521 DOI: 10.1016/j.isci.2023.106195] [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: 04/12/2022] [Revised: 12/05/2022] [Accepted: 02/08/2023] [Indexed: 02/15/2023] Open
Abstract
Aberrant mechanotransduction and compromised epithelial barrier function are associated with numerous human pathologies including inflammatory skin disorders. However, the cytoskeletal mechanisms regulating inflammatory responses in the epidermis are not well understood. Here we addressed this question by inducing a psoriatic phenotype in human keratinocytes and reconstructed human epidermis using a cytokine stimulation model. We show that the inflammation upregulates the Rho-myosin II pathway and destabilizes adherens junctions (AJs) promoting YAP nuclear entry. The integrity of cell-cell adhesion but not the myosin II contractility per se is the determinative factor for the YAP regulation in epidermal keratinocytes. The inflammation-induced disruption of AJs, increased paracellular permeability, and YAP nuclear translocation are regulated by ROCK2, independently from myosin II activation. Using a specific inhibitor KD025, we show that ROCK2 executes its effects via cytoskeletal and transcription-dependent mechanisms to shape the inflammatory response in the epidermis.
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Affiliation(s)
- Maria S. Shutova
- University of Geneva, Department of Pathology and Immunology, Geneva, Switzerland
- University Hospitals of Geneva, Division of Dermatology and Venereology, Geneva, Switzerland
- Geneva Centre for Inflammation Research, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Julia Borowczyk
- University of Geneva, Department of Pathology and Immunology, Geneva, Switzerland
| | - Barbara Russo
- University of Geneva, Department of Pathology and Immunology, Geneva, Switzerland
- University Hospitals of Geneva, Division of Dermatology and Venereology, Geneva, Switzerland
- Geneva Centre for Inflammation Research, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Sihem Sellami
- University of Geneva, Department of Pathology and Immunology, Geneva, Switzerland
| | - Justyna Drukala
- Jagiellonian University, Department of Cell Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Cracow, Poland
| | - Michal Wolnicki
- Department of Pediatric Urology, Jagiellonian University Medical College, Cracow, Poland
| | - Nicolo C. Brembilla
- University Hospitals of Geneva, Division of Dermatology and Venereology, Geneva, Switzerland
- Geneva Centre for Inflammation Research, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Gurkan Kaya
- University Hospitals of Geneva, Division of Dermatology and Venereology, Geneva, Switzerland
| | - Andrei I. Ivanov
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Wolf-Henning Boehncke
- University of Geneva, Department of Pathology and Immunology, Geneva, Switzerland
- University Hospitals of Geneva, Division of Dermatology and Venereology, Geneva, Switzerland
- Geneva Centre for Inflammation Research, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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Butter R, Halfwerk H, Radonic T, Lissenberg-Witte B, Thunnissen E. The impact of impaired tissue fixation in resected non-small-cell lung cancer on protein deterioration and DNA degradation. Lung Cancer 2023; 178:108-115. [PMID: 36812759 DOI: 10.1016/j.lungcan.2023.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/25/2023] [Accepted: 02/08/2023] [Indexed: 02/13/2023]
Abstract
OBJECTIVES The objective is to assess the impact of the quality of tissue fixation in surgical pathology on immunohistochemical (IHC) staining and DNA degradation. MATERIALS AND METHODS Twenty-five non-small cell lung cancer (NSCLC) resection specimens were analyzed. After resection, all tumors were processed according to the protocols in our center. In haematoxylin and eosin (H&E) stained tissue slides, adequately- and inadequately fixed tumor areas were microscopically demarcated, based on basement membrane detachment. In 10 IHC stains ALK (clone 5A4), PD-L (clone 22C3), CAM5.2, CK7, c-Met, KER-MNF116, NapsinA, p40, ROS1, TTF1) the immunoreactivity in H-scores was determined in adequately- and inadequately fixed, and necrotic tumor areas. From the same areas DNA was isolated, and DNA fragmentation in base pairs (bp) was measured. RESULTS H-scores were significantly higher in H&E adequately fixed tumor areas in IHC stains KER-MNF116 (H-score 256 vs 15, p=0.001) and p40 (H-score 293 vs 248, p=0.028). All other stains showed a trend towards higher immunoreactivity in H&E adequately fixed areas. Independent of H&E adequatelty- or inadequately fixed areas, all IHC stains showed significant different IHC staining intensity within tumors, suggesting heterogeneous immunoreactivity (H-scores: PD-L1 123 vs 6, p = 0.001; CAM5.2 242 vs 101, p=<0.001; CK7 242 vs 128, p=<0.001; c-MET 99 vs 20, p=<0.001; KER-MNF116 281 vs 120, p=<0.001; Napsin A 268 vs 130, p = 0.005; p40 292 vs 166, p = 0.008; TTF1 199 vs 63, p=<0.001). DNA fragments rarely exceeded a length of 300 bp, independent of adequate fixation. However, DNA fragments of 300 and 400 bp had higher concentrations in tumors with short fixation delay (<6 h vs >16 h) and short fixation time (<24 h vs >24 h). CONCLUSIONS Impaired tissue fixation of resected lung tumors results in decreased IHC staining intensity in some parts of the tumor. This may impact the reliability of IHC analysis.
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Affiliation(s)
- Rogier Butter
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Hans Halfwerk
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Teodora Radonic
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University Amsterdam, Amsterdam, The Netherlands
| | - Birgit Lissenberg-Witte
- Department of Epidemiology and Data Science, Amsterdam University Medical Centers, VU University Amsterdam, Amsterdam, The Netherlands
| | - Erik Thunnissen
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University Amsterdam, Amsterdam, The Netherlands.
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5
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Chiriboga L, Callis GM, Wang Y, Chlipala E. Guide for collecting and reporting metadata on protocol variables and parameters from slide-based histotechnology assays to enhance reproducibility. J Histotechnol 2022; 45:132-147. [DOI: 10.1080/01478885.2022.2134022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Luis Chiriboga
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
- NYULH Center for Biospecimen Research and Development, New York, NY, USA
| | | | - Yongfu Wang
- Stowers Institute for Medical Research, Kansas, MO, USA
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6
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Marshall JL, Peshkin BN, Yoshino T, Vowinckel J, Danielsen HE, Melino G, Tsamardinos I, Haudenschild C, Kerr DJ, Sampaio C, Rha SY, FitzGerald KT, Holland EC, Gallagher D, Garcia-Foncillas J, Juhl H. OUP accepted manuscript. Oncologist 2022; 27:272-284. [PMID: 35380712 PMCID: PMC8982374 DOI: 10.1093/oncolo/oyab048] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/05/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- John L Marshall
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
- Corresponding author: John L. Marshall, MD, The Ruesch Center for the Cure of Gastrointestinal Cancers, Frederick P. Smith Endowed Chair, Chief, Hematology and Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, 3800 Reservoir Road, Washington, DC 20007, USA. Tel: +1 202 444 2223;
| | - Beth N Peshkin
- Georgetown University, Lombardi Comprehensive Cancer Center, Washington, DC, USA
| | | | | | - Håvard E Danielsen
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, Radiumhospitalet, Montebello, Oslo, Norway
| | - Gerry Melino
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, Rome, Italy
| | - Ioannis Tsamardinos
- JADBio Gnosis DA, N. Plastira 100, Science and Technology Park of Crete and Institute of Applied and Computational Mathematics, Foundation for Research and Technology Hellas, Heraklion, GR, Greece
| | | | - David J Kerr
- Nuffield Division of Clinical and Laboratory Sciences, Level 4, Academic Block, John Radcliffe Infirmary, Headington, Oxford, UK
| | | | - Sun Young Rha
- Yonsei Cancer Center, Yonsei University College of Medicine, Seodaemun-Ku, Seoul, Korea
| | - Kevin T FitzGerald
- Department of Medical Humanities in the School of Medicine, Creighton University, Omaha, NE, USA
| | - Eric C Holland
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - David Gallagher
- St. James’s Hospital/Trinity College Dublin, St. Raphael’s House, Dublin, Ireland
| | - Jesus Garcia-Foncillas
- Cancer Institute, Fundacion Jimenez Diaz University Hospital, Autonomous University, Madrid, Spain
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7
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Effect of immediate cold formalin fixation on phosphoprotein IHC tumor biomarker signal in liver tumors using a cold transport device. Sci Rep 2020; 10:2147. [PMID: 32034185 PMCID: PMC7005752 DOI: 10.1038/s41598-020-58257-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/13/2020] [Indexed: 11/08/2022] Open
Abstract
Phosphoproteins are the key indicators of signaling network pathway activation. Many disease treatment therapies are designed to inhibit these pathways and effective diagnostics are required to evaluate the efficacy of these treatments. Phosphoprotein IHC have been impractical for diagnostics due to inconsistent results occurring from technical limitations. We have designed and tested a novel cold transport device and rapid cold plus warm formalin fixation protocol using phosphoproteins IHC. We collected 50 liver tumors that were split into two experimental conditions: 2 + 2 rapid fixation (2 hours cold then 2 hour warm formalin) or 4 hour room-temperature formalin. We analyzed primary hepatocellular carcinoma (n = 10) and metastatic gastrointestinal tumors (n = 28) for phosphoprotein IHC markers pAKT, pERK, pSRC, pSTAT3, and pSMAD2 and compared them to slides obtained from the clinical blocks. Expression of pERK and pSRC, present in the metastatic colorectal carcinoma, were better preserved with the rapid processing protocol while pSTAT3 expression was detected in hepatocellular carcinoma. Differences in pSMAD2 expression were difficult to detect due to the ubiquitous nature of protein expression. There were only 3 cases expressing pAKT and all exhibited a dramatic loss of signal for the standard clinical workflow. The rapid cold preservation shows improvement in phosphoprotein preservation.
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8
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Lerch M, Kenerson H, Theiss A, Chafin D, Westerhoff M, Otter M, Yeung R, Baird G. Rapid tissue processing using a temperature-controlled collection device to preserve tumor biomarkers. Cell Tissue Bank 2019; 21:89-97. [PMID: 31838727 PMCID: PMC7058599 DOI: 10.1007/s10561-019-09800-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 12/09/2019] [Indexed: 02/07/2023]
Abstract
Precision tissue diagnostics rely on high quality input specimens so that assay results are not affected by artifact, but advances in collection and processing of tissue specimens have lagged behind innovations in diagnostic assay development. Therefore, we have designed and evaluated a novel surgical tissue collection device that maintains and monitors sample temperature and motion throughout transport so that the major preanalytical variable of tissue temperature can be controlled and measured. This device, in combination with an improved cold–hot tissue fixation protocol affords optimal biomarker preservation in less overall time, thereby simultaneously improving diagnostic quality and turnaround time. We collected 50 primary and metastatic liver tumors using a novel transport device. Tissue was fixed using a rapid cold–hot fixation protocol and immunohistochemical assays were used to assess the performance of the device, in comparison to control tissue preserved using standard clinical fixation protocol. Two pathologists evaluated the IHC studies in a blinded fashion to determine the immunophenotype of each tumor. The observed IHC staining intensities and the clinical impressions of the immunophenotypes did not differ between tissue collected with the novel device and control tissue, while improvements in processing time were achieved. The novel cold transport device and rapid fixation protocol can be successfully and safely combined and used to monitor specimen conditions, thus preserving the diagnostic utility of specimens and improving the overall turn-around time of the diagnostic process.
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Affiliation(s)
- Melissa Lerch
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, WA, USA
| | - Heidi Kenerson
- Department of Surgery, University of Washington Medical Center, Seattle, WA, USA
| | - Abbey Theiss
- Ventana Medical Systems, Inc., 1910 Innovation Parkway, Tucson, AZ, USA
| | - David Chafin
- Ventana Medical Systems, Inc., 1910 Innovation Parkway, Tucson, AZ, USA
| | - Maria Westerhoff
- Department of Pathology, University of Washington Medical Center, 1959 NE Pacific St., Seattle, WA, USA
| | - Michael Otter
- Ventana Medical Systems, Inc., 1910 Innovation Parkway, Tucson, AZ, USA
| | - Raymond Yeung
- Department of Surgery, University of Washington Medical Center, Seattle, WA, USA
| | - Geoffrey Baird
- Department of Laboratory Medicine, University of Washington Medical Center, Seattle, WA, USA.
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Abstract
Castration-resistant prostate cancer (CRPC) remains incurable despite the approval of several new treatments. Identification of new biomarkers and therapeutic targets to enable personalization of CRPC therapy, with the aim of maximizing therapeutic responses and minimizing toxicity in patients, is urgently needed. Prostate cancer progression and therapeutic resistance are frequently driven by aberrantly activated kinase signalling pathways that are amenable to pharmacological inhibition. Personalized phosphoproteomics, which enables the analysis of signalling networks in individual tumours, is a promising approach to advance personalized therapy by discovering biomarkers of pathway activity and clinically actionable targets. Several technologies for global and targeted phosphoproteomic analysis exist, each with its own strengths and shortcomings. Global discovery phosphoproteomics is predominantly conducted using liquid chromatography-tandem mass spectrometry coupled with data-dependent or data-independent acquisition technologies. Multiplexed targeted phosphoproteomics can be divided into platforms based on mass spectrometry or antibodies, including selected or parallel reaction monitoring and triggered by offset, multiplexed, accurate mass, high-resolution, absolute quantification (known as TOMAHAQ) or forward-phase or reverse-phase protein arrays, respectively. Several obstacles still need to be overcome before the full potential of phosphoproteomics can be realized in routine clinical practice, but a future phosphoproteomics-centric trans-omic profiling approach should enable optimized personalized CRPC management through improved biomarkers and targeted treatments.
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10
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Neumeister VM, Juhl H. Tumor Pre-Analytics in Molecular Pathology: Impact on Protein Expression and Analysis. CURRENT PATHOBIOLOGY REPORTS 2018; 6:265-274. [PMID: 30595971 PMCID: PMC6290693 DOI: 10.1007/s40139-018-0179-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Purpose of Review Precision medicine promises patient tailored, individualized diagnosis and treatment of diseases and relies on clinical specimen integrity and accuracy of companion diagnostic testing. Therefore, pre-analytics, which are defined as the collection, processing, and storage of clinical specimens, are critically important to enable optimal diagnostics, molecular profiling, and clinical decision-making around harvested specimens. This review article discusses the impact of tumor pre-analytics on molecular pathology focusing on biospecimen protein expression and analysis. Recent Findings Due to busy clinical schedules and workflows that have been established for many years and to lack of standardization and limited assessment tools to quantify variability in pre-analytical processing, the effects of pre-analytics on biospecimen integrity are often overlooked. Several studies have recently emphasized an emerging crisis in science and reproducibility of results. Summary Biomarker instability due to pre-analytical variables affects comprehensive analysis and molecular phenotyping of patients’ tissue. This problematic emphasizes the critical need for standardized protocols and technologies to be applied in the clinical and research setting.
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Affiliation(s)
| | - Hartmut Juhl
- Indivumed, GmbH, Falkenried 88, D-20251 Hamburg, Germany
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11
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Agrawal L, Engel KB, Greytak SR, Moore HM. Understanding preanalytical variables and their effects on clinical biomarkers of oncology and immunotherapy. Semin Cancer Biol 2017; 52:26-38. [PMID: 29258857 DOI: 10.1016/j.semcancer.2017.12.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/07/2017] [Accepted: 12/13/2017] [Indexed: 12/20/2022]
Abstract
Identifying a suitable course of immunotherapy treatment for a given patient as well as monitoring treatment response is heavily reliant on biomarkers detected and quantified in blood and tissue biospecimens. Suboptimal or variable biospecimen collection, processing, and storage practices have the potential to alter clinically relevant biomarkers, including those used in cancer immunotherapy. In the present review, we summarize effects reported for immunologically relevant biomarkers and highlight preanalytical factors associated with specific analytical platforms and assays used to predict and gauge immunotherapy response. Given that many of the effects introduced by preanalytical variability are gene-, transcript-, and protein-specific, biospecimen practices should be standardized and validated for each biomarker and assay to ensure accurate results and facilitate clinical implementation of newly identified immunotherapy approaches.
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Affiliation(s)
- Lokesh Agrawal
- Biorepositories and Biospecimen Research Branch (BBRB), Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Drive, Bethesda, Maryland, USA
| | | | | | - Helen M Moore
- Biorepositories and Biospecimen Research Branch (BBRB), Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Drive, Bethesda, Maryland, USA.
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12
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Donovan MJ, Cordon-Cardo C. Implementation of a Precision Pathology Program Focused on Oncology-Based Prognostic and Predictive Outcomes. Mol Diagn Ther 2017; 21:115-123. [PMID: 28000172 DOI: 10.1007/s40291-016-0249-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Personalized or precision medicine as a diagnostic and therapeutic paradigm was introduced some 10-15 years ago, with the advent of biomarker discovery as a mechanism for identifying prognostic and predictive attributes associated with treatment indication and outcome. While the concept is not new, the successful development and implementation of novel 'companion diagnostics', especially in oncology, continues to represent a significant challenge and is currently at the forefront of smart trial design and therapeutic choice. The ability to determine patient selection for a specific therapy has broad implications including better chances for a positive outcome, limited exposure to potentially toxic drugs and improved health economics. Importantly, a significant step in this paradigm is the role of predictive pathology or the accurate assessment of morphology at the microscopic level. In breast cancer, this has been most useful where histologic attributes such as the classification of tubular and cribriform carcinoma dictates surgery while neoadjuvant studies suggest that patients with lobular carcinoma are not likely to benefit from chemotherapy. The next level of 'personalized pathology' at the tissue-cellular level is the use of 'protein biomarker panels' to classify the disease process and ultimately drive tumor characterization and treatment. The following review article will focus on the evolution of predictive pathology from a subjective, 'opinion-based' approach to a quantitative science. In addition, we will discuss the individual components of the precise pathology platform including advanced image analysis, biomarker quantitation with mathematical modeling and the integration with fluid-based (i.e. blood, urine) analytics as drivers of next generation precise patient phenotyping.
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13
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Srivastava AK, Hollingshead MG, Weiner J, Navas T, Evrard YA, Khin SA, Ji JJ, Zhang Y, Borgel S, Pfister TD, Kinders RJ, Bottaro DP, Linehan WM, Tomaszewski JE, Doroshow JH, Parchment RE. Pharmacodynamic Response of the MET/HGF Receptor to Small-Molecule Tyrosine Kinase Inhibitors Examined with Validated, Fit-for-Clinic Immunoassays. Clin Cancer Res 2016; 22:3683-94. [PMID: 27001313 PMCID: PMC7802886 DOI: 10.1158/1078-0432.ccr-15-2323] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 02/23/2016] [Indexed: 01/08/2023]
Abstract
PURPOSE Rational development of targeted MET inhibitors for cancer treatment requires a quantitative understanding of target pharmacodynamics, including molecular target engagement, mechanism of action, and duration of effect. EXPERIMENTAL DESIGN Sandwich immunoassays and specimen handling procedures were developed and validated for quantifying full-length MET and its key phosphospecies (pMET) in core tumor biopsies. MET was captured using an antibody to the extracellular domain and then probed using antibodies to its C-terminus (full-length) and epitopes containing pY1234/1235, pY1235, and pY1356. Using pMET:MET ratios as assay endpoints, MET inhibitor pharmacodynamics were characterized in MET-amplified and -compensated (VEGFR blockade) models. RESULTS By limiting cold ischemia time to less than two minutes, the pharmacodynamic effects of the MET inhibitors PHA665752 and PF02341066 (crizotinib) were quantifiable using core needle biopsies of human gastric carcinoma xenografts (GTL-16 and SNU5). One dose decreased pY1234/1235 MET:MET, pY1235-MET:MET, and pY1356-MET:MET ratios by 60% to 80% within 4 hours, but this effect was not fully sustained despite continued daily dosing. VEGFR blockade by pazopanib increased pY1235-MET:MET and pY1356-MET:MET ratios, which was reversed by tivantinib. Full-length MET was quantifiable in 5 of 5 core needle samples obtained from a resected hereditary papillary renal carcinoma, but the levels of pMET species were near the assay lower limit of quantitation. CONCLUSIONS These validated immunoassays for pharmacodynamic biomarkers of MET signaling are suitable for studying MET responses in amplified cancers as well as compensatory responses to VEGFR blockade. Incorporating pharmacodynamic biomarker studies into clinical trials of MET inhibitors could provide critical proof of mechanism and proof of concept for the field. Clin Cancer Res; 22(14); 3683-94. ©2016 AACR.
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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
| | - Melinda G Hollingshead
- Biological Testing Branch, Developmental Therapeutics Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Jennifer Weiner
- Laboratory of Human Toxicology and Pharmacology, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Tony Navas
- Laboratory of Human Toxicology and Pharmacology, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Yvonne A Evrard
- Laboratory of Human Toxicology and Pharmacology, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Sonny A Khin
- Laboratory of Human Toxicology and Pharmacology, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Jiuping Jay Ji
- National Clinical Target Validation Laboratory, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Yiping Zhang
- National Clinical Target Validation Laboratory, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Suzanne Borgel
- In Vivo Evaluation Group, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Thomas D Pfister
- Laboratory of Human Toxicology and Pharmacology, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Robert J Kinders
- Laboratory of Human Toxicology and Pharmacology, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | | | | | | | - James H Doroshow
- Division of Cancer Treatment and Diagnosis, NCI, Bethesda, Maryland
| | - 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.
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14
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Chafin D. Two-temperature formalin fixation preserves activation states efficiently. Recent Results Cancer Res 2015; 199:107-17. [PMID: 25636434 DOI: 10.1007/978-3-319-13957-9_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Modern pathology is built around the principle of preserving tissues such that the in vivo molecular status is maintained at levels representative of the disease state. Tissues are immersed in a solution of fixative which slowly inactivates biological activities, thus preserving the sample. Further processing ultimately allows the tissue to be embedded into wax for thin sectioning and staining for interpretation microscopically. Every year, around 7 billion tissue samples are submitted for processing in the United States alone. With this huge workload, histology laboratories are looking for faster methods of performing fixation, which currently require from several hours to days to complete. Ideally, this procedure could be standardized and would be quicker with better preservation over a wide range of biologically relevant molecules.
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Affiliation(s)
- David Chafin
- , 1910 East Innovation PARK Drive, Oro Valley, AZ, 85755, USA,
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15
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Donovan MJ, Cordon-Cardo C. Overcoming tumor heterogeneity in the molecular diagnosis of urological cancers. Expert Rev Mol Diagn 2014; 14:1023-31. [PMID: 25327491 DOI: 10.1586/14737159.2014.965151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Our understanding of tumor heterogeneity and impact on treatment response is still in its infancy, presenting significant challenges to the molecular pathologist, treating physician and ultimately for the patient. Given that tumor recurrence due to treatment resistance is the most common cause of cancer death, there remains a critical unmet need to change the current paradigm. The mechanisms which underlie tumor heterogeneity can be broadly divided into genomic instability and non-mutational processes, including stochastic variations in cellular responses, modulation by tumor microenvironment and or phenotypic/ functional plasticity relating to cancer stem cells. We believe that these biological mechanisms are not mutually exclusive and emphasize the need for more suitable methodologies to exploit the spatiotemporal patterns of intratumoral heterogeneity using novel approaches such as quantitative tissue-based biomarker assessment and systemic fluid analytics. Generating a comprehensive patient-centric phenotypic disease profile should generate a 'codex' which can be employed to change the current treatment decision process.
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Affiliation(s)
- Michael J Donovan
- Department of Pathology, Icahn School of Medicine, 1468 Madison Avenue, New York City, NY 10029, USA
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