1
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Shen Y, Zhang X, Zhang L, Zhang Z, Lyu B, Lai Q, Li Q, Zhang Y, Ying J, Song J. Performance evaluation of a CRISPR Cas9-based selective exponential amplification assay for the detection of KRAS mutations in plasma of patients with advanced pancreatic cancer. J Clin Pathol 2023:jcp-2023-208974. [PMID: 37679033 DOI: 10.1136/jcp-2023-208974] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/21/2023] [Indexed: 09/09/2023]
Abstract
AIMS Pancreatic ductal adenocarcinoma (PDAC) is highly malignant, with shockingly mortality rates. KRAS oncoprotein is the main molecular target for PDAC. Liquid biopsies, such as the detection of circulating tumour DNA (ctDNA), offer a promising approach for less invasive diagnosis. In this study, we aim to evaluate the precision and utility of programmable enzyme-based selective exponential amplification (PASEA) assay for rare mutant alleles identification. METHODS PASEA uses CRISPR-Cas9 to continuously shear wild-type alleles during recombinase polymerase amplification, while mutant alleles are exponentially amplified, ultimately reaching a level detectable by Sanger sequencing. We applied PASEA to detect KRAS mutations in plasma ctDNA. A total of 153 patients with stage IV PDAC were enrolled. We investigated the relationship between ctDNA detection rates with various clinical factors. RESULTS Our results showed 91.43% vs 44.83% detection rate in patients of prechemotherapy and undergoing chemotherapy. KRAS ctDNA was more prevalent in patients with liver metastases and patients did not undergo surgical resection. Patients with liver metastases prior to chemotherapy showed a sensitivity of 95.24% (20/21) with PASEA. Through longitudinal monitoring, we found ctDNA may be a more accurate biomarker for monitoring chemotherapy efficacy in PDAC than CA19-9. CONCLUSIONS Our study sheds light on the potential of ctDNA as a valuable complementary biomarker for precision targeted therapy, emphasising the importance of considering chemotherapy status, metastatic sites and surgical history when evaluating its diagnostic potential in PDAC. PASEA technology provides a reliable, cost-effective and minimally invasive method for detecting ctDNA of PDAC.
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Affiliation(s)
- Yue Shen
- School of life sciences, Tianjin University, Tianjin, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Xiaoling Zhang
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Liyi Zhang
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Zuoying Zhang
- School of life sciences, Tianjin University, Tianjin, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Bao Lyu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Qian Lai
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Qinglin Li
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Yuhua Zhang
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Jieer Ying
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Jinzhao Song
- School of life sciences, Tianjin University, Tianjin, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
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2
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Shimazawa R, Ikeda M. Regulatory perspectives on next-generation sequencing and complementary diagnostics in Japan. Expert Rev Mol Diagn 2020; 20:601-610. [DOI: 10.1080/14737159.2020.1728256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Rumiko Shimazawa
- Department of Clinical Pharmacology, Tokai University School of Medicine, Isehara, Japan
| | - Masayuki Ikeda
- Department of Medical Informatics, Kagawa University Hospital, Takamatsu, Japan
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3
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Liang B, Yu K, Ling Y, Kolios M, Exner A, Wang Z, Hu B, Zuo G, Chen Y, Zheng Y. An artificially engineered "tumor bio-magnet" for collecting blood-circulating nanoparticles and magnetic hyperthermia. Biomater Sci 2019; 7:1815-1824. [PMID: 30916668 DOI: 10.1039/c8bm01658e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
It is a great challenge to directly endow a tumor with specific functions for theranostic treatment. In this study, we report on a novel approach to transform a tumor into a "bio-magnet", to be magnetized on demand, in order to create an intrinsic tumor magnetic field that would collect magnetic nanoparticles (MNPs) circulating in the blood and achieve simultaneous magnetic hyperthermia. This was achieved by the localized intratumoral injection of liquid Nd2Fe14B/Fe3O4-PLGA, followed by solvent exchange that induces a liquid-to-solid transformation. After the magnetism charging process, the solid Nd2Fe14B/Fe3O4-PLGA implant was endowed with permanent magnetic properties and in situ created the magnetic field within the tumor tissue, making the tumor a "bio-magnet". After the creation of the bio-magnet, intravenously injected MNPs accumulated into the tumor tissue due to the tumor magnetic field. Importantly, both the in vitro and ex vivo results demonstrated the high efficiency of the implanted bio-magnet for magnetic hyperthermia. This new approach achieves magnetic targeting by creating a tumor "bio-magnet", which generates a strong magnetic field within the tumor, paving a new way for the development of an efficient targeting strategy for tumor therapy.
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Affiliation(s)
- Bing Liang
- Institute of Ultrasound Imaging of Chongqing Medical University, Second Affiliated Hospital of Chongqing Medical University, 76 Linjiang Road, Yuzhong Distinct, Chongqing, 400010, P. R. China.
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4
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Renfro LA, An MW, Mandrekar SJ. Precision oncology: A new era of cancer clinical trials. Cancer Lett 2017; 387:121-126. [PMID: 26987624 PMCID: PMC5023449 DOI: 10.1016/j.canlet.2016.03.015] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 03/07/2016] [Accepted: 03/08/2016] [Indexed: 01/13/2023]
Abstract
Traditionally, site of disease and anatomic staging have been used to define patient populations to be studied in individual cancer clinical trials. In the past decade, however, oncology has become increasingly understood on a cellular and molecular level, with many cancer subtypes being described as a function of biomarkers or tumor genetic mutations. With these changes in the science of oncology have come changes to the way we design and perform clinical trials. Increasingly common are trials tailored to detect enhanced efficacy in a patient subpopulation, e.g. patients with a known biomarker value or whose tumors harbor a specific genetic mutation. Here, we provide an overview of traditional and newer biomarker-based trial designs, and highlight lessons learned through implementation of several ongoing and recently completed trials.
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Affiliation(s)
- Lindsay A Renfro
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA.
| | - Ming-Wen An
- Department of Mathematics and Statistics, Vassar College, Poughkeepsie, NY, USA
| | - Sumithra J Mandrekar
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
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5
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Jørgensen JT, Hersom M. Companion diagnostics-a tool to improve pharmacotherapy. ANNALS OF TRANSLATIONAL MEDICINE 2016; 4:482. [PMID: 28149844 PMCID: PMC5233535 DOI: 10.21037/atm.2016.12.26] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The variability of pharmacotherapy can be of a significant magnitude, and the main reason for this is often diseases heterogeneity. Patients who have similar diagnoses very often respond differently to the same pharmacological intervention, with great variability in both efficacy and safety outcome. Despite having discussed personalized medicine for more than a decade, we still see that most drug prescriptions for severe chronic diseases are largely based on 'trial and error' and not on solid biomarker data. However, with the advance of molecular diagnostics and a subsequent increased understanding of disease mechanisms, things are slowly changing. Within the last few years, we have seen an increasing number of predictive biomarker assays being developed to guide the use of targeted cancer drugs. This type of assay is called companion diagnostics and is developed in parallel to the drug using the drug-diagnostic co-development model. The development of companion diagnostics is a relatively new discipline and in this review, different aspects will be discussed including clinical and regulatory issues. Furthermore, examples of drugs, such as the ALK and PD-1/PD-L1 inhibitors, that have been approved recently together with a companion or complimentary diagnostic will be given.
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Affiliation(s)
| | - Maria Hersom
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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6
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Enzmann H, Meyer R, Broich K. The new EU regulation on in vitro diagnostics: potential issues at the interface of medicines and companion diagnostics. Biomark Med 2016; 10:1261-1268. [DOI: 10.2217/bmm-2016-0233] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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7
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Viale G, Paterson J, Bloch M, Csathy G, Allen D, Dell'Orto P, Kjærsgaard G, Levy YY, Jørgensen JT. Assessment of HER2 amplification status in breast cancer using a new automated HER2 IQFISH pharmDx™ (Dako Omnis) assay. Pathol Res Pract 2016; 212:735-42. [PMID: 27461826 DOI: 10.1016/j.prp.2016.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 05/09/2016] [Accepted: 06/08/2016] [Indexed: 10/21/2022]
Abstract
In breast cancer the human epidermal growth factor receptor 2 (HER2) is an important target for a number of different HER2 inhibitors. Different slide-based assays are available for assessment of treatment eligibility, which include fluorescence in situ hybridization (FISH) or other in situ hybridization (ISH) methods for assessment of the HER2 gene status. Here we report a summary of the validation data on HER2 IQFISH pharmDx™ (Dako Omnis), a newly developed assay for the automated staining platform Dako Omnis. The assay uses a non-toxic buffer that significantly reduces the hybridization time, which results in a total turnaround time of 3½ to 4h from deparaffinization to counting of the gene and centromere signals. The data reported in the current summary covers method comparison, assessment of staining quality, observer-to-observer reproducibility as well as reproducibility within and between laboratories. Based on data from the different studies it was concluded that HER2 IQFISH pharmDx (Dako Omnis) is a reliable and robust assay with a high precision that is at least comparable to the manual HER2 IQFISH pharmDx™ assay and the PathVysion(®)HER-2 DNA Probe Kit.
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Affiliation(s)
- Giuseppe Viale
- University of Milan, Istituto Europeo di Oncologia, Milan, Italy
| | | | - Miriam Bloch
- Clarient Pathology Services, Aliso Viejo, CA, USA
| | | | | | | | | | - Yaron Y Levy
- Dako, An Agilent Technologies Company, Glostrup, Denmark
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8
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Abstract
Companion diagnostics (CDx) is a positive attempt in the direction of improving the drug development process, especially in the field of oncology, with the advent of newer targeted therapies. It helps the oncologist in deciding the choice of treatment for the individual patient. The role of CDx assays has attracted the attention of regulators, and especially the US Food and Drug Administration developed regulatory strategies for CDx and the drug-diagnostic codevelopment project. For an increasing number of cancer patients, the treatment selection will depend on the result generated by a CDx assay, and consequently this type of assay has become critical for the care and safety of the patients. In addition to the assay-based approach, molecular imaging with its ability to image at the genetic and receptor level has made foray into the field of drug development and personalized medicine. We shall review these aspects of CDx, with special focus on molecular imaging and the upcoming concept of Theranostics.
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9
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Luo D, Smith JA, Meadows NA, Schuh A, Manescu KE, Bure K, Davies B, Horne R, Kope M, DiGiusto DL, Brindley DA. A Quantitative Assessment of Factors Affecting the Technological Development and Adoption of Companion Diagnostics. Front Genet 2016; 6:357. [PMID: 26858745 PMCID: PMC4730156 DOI: 10.3389/fgene.2015.00357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/10/2015] [Indexed: 12/28/2022] Open
Abstract
Rapid innovation in (epi)genetics and biomarker sciences is driving a new drug development and product development pathway, with the personalized medicine era dominated by biologic therapeutics and companion diagnostics. Companion diagnostics (CDx) are tests and assays that detect biomarkers and specific mutations to elucidate disease pathways, stratify patient populations, and target drug therapies. CDx can substantially influence the development and regulatory approval for certain high-risk biologics. However, despite the increasingly important role of companion diagnostics in the realization of personalized medicine, in the USA, there are only 23 Food and Drug Administration (FDA) approved companion diagnostics on the market for 11 unique indications. Personalized medicines have great potential, yet their use is currently constrained. A major factor for this may lie in the increased complexity of the companion diagnostic and corresponding therapeutic development and adoption pathways. Understanding the market dynamics of companion diagnostic/therapeutic (CDx/Rx) pairs is important to further development and adoption of personalized medicine. Therefore, data collected on a variety of factors may highlight incentives or disincentives driving the development of companion diagnostics. Statistical analysis for 36 hypotheses resulted in two significant relationships and 34 non-significant relationships. The sensitivity of the companion diagnostic was the only factor that significantly correlated with the price of the companion diagnostic. This result indicates that while there is regulatory pressure for the diagnostic and pharmaceutical industry to collaborate and co-develop companion diagnostics for the approval of personalized therapeutics, there seems to be a lack of parallel economic collaboration to incentivize development of companion diagnostics.
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Affiliation(s)
- Dee Luo
- Department of Biological Basis of Behavior, University of Pennsylvania Phildephila, PA, USA
| | - James A Smith
- The Oxford - UCL Centre for the Advancement of Sustainable Medical Innovation, University of OxfordOxford, UK; Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of OxfordOxford, UK
| | | | - A Schuh
- National Institute of Health Research, Biomedical Research Centre, Molecular Diagnostic Centre, Oxford University Hospitals Oxford, UK
| | - Katie E Manescu
- Department of Biochemical Engineering, University College London London, UK
| | - Kim Bure
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford Oxford, UK
| | | | - Rob Horne
- The UCL School of Pharmacy, University College London London, UK
| | - Mike Kope
- SENS Research Foundation Mountain View, CA, USA
| | - David L DiGiusto
- Stem Cell and Cellular Therapeutics Operations at Stanford University Hospital and Clinic Stanford, CA, USA
| | - David A Brindley
- Stem Cell and Cellular Therapeutics Operations at Stanford University Hospital and ClinicStanford, CA, USA; The Oxford - UCL Centre for the Advancement of Sustainable Medical Innovation, University of OxfordOxford, UK; Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of OxfordOxford, UK; USCF-Stanford Center of Excellence in Regulatory Science and InnovationSan Francisco, CA, USA; Centre for Behavioural Medicine, UCL School of Pharmacy, University College LondonLondon, UK; Harvard Stem Cell InstituteCambridge, MA, USA
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10
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Shimazawa R, Ikeda M. Drug–diagnostic co-development: challenges and issues. Expert Rev Mol Diagn 2016; 16:187-204. [DOI: 10.1586/14737159.2016.1132163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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11
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Abstract
The immune checkpoint inhibitors pembrolizumab and nivolumab together with their diagnostic assays have recently been granted market authorization for treatment of advanced non-small-cell lung cancer in the USA. The two assays, PD-L1 IHC 22C3 pharmDx and PD-L1 IHC 28-8 pharmDx (both by Dako, Glostrup, Denmark), are the first PD-L1 IHC assays to obtain regulatory approval through the Premarket Approval process. This approval is supported by recent clinical studies that have shown a positive correlation between PD-L1 expression and the outcome following treatment with different PD-1/PD-L1 checkpoint inhibitors. These diagnostic assays are able to identify the group of non-small-cell lung cancer patients who will benefit most from treatment with the immune checkpoint inhibitors. However, so far, it is only the PD-L1 IHC 22C3 pharmDx assay, which is linked to the use of pembrolizumab, that has obtained regulatory status as a companion diagnostic.
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12
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Yeat NC, Lin C, Sager M, Lin J. Cancer proteomics: developments in technology, clinical use and commercialization. Expert Rev Proteomics 2015; 12:391-405. [PMID: 26145529 DOI: 10.1586/14789450.2015.1051969] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In the last two decades, advances in genomic, transcriptomic and proteomic methods have enabled us to identify and classify cancers by their molecular profiles. Many anticipate that a molecular taxonomy of cancer will not only lead to more effective subtyping of cancers but also earlier diagnoses, more informative prognoses and more targeted treatments. This article reviews recent technological developments in the field of proteomics, recent discoveries in proteomic cancer biomarker research and trends in clinical use. Readers are also informed of examples of successful commercialization, and the future of proteomics in cancer diagnostics.
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Affiliation(s)
- Nai Chien Yeat
- Rare Genomics Institute, 4100 Forest Park, St. Louis, MO 63108, USA
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13
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14
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Percy AJ, Yang J, Chambers AG, Simon R, Hardie DB, Borchers CH. Multiplexed MRM with Internal Standards for Cerebrospinal Fluid Candidate Protein Biomarker Quantitation. J Proteome Res 2014; 13:3733-3747. [DOI: 10.1021/pr500317d] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Andrew J. Percy
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Juncong Yang
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Andrew G. Chambers
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Romain Simon
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Darryl B. Hardie
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Christoph H. Borchers
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
- Department
of Biochemistry and Microbiology, University of Victoria, Petch Building
Room 207, 3800 Finnerty Road, Victoria, BC V8P 5C2, Canada
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15
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Goltsov A, Deeni Y, Khalil HS, Soininen T, Kyriakidis S, Hu H, Langdon SP, Harrison DJ, Bown J. Systems analysis of drug-induced receptor tyrosine kinase reprogramming following targeted mono- and combination anti-cancer therapy. Cells 2014; 3:563-91. [PMID: 24918976 PMCID: PMC4092865 DOI: 10.3390/cells3020563] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 05/14/2014] [Accepted: 05/19/2014] [Indexed: 12/12/2022] Open
Abstract
The receptor tyrosine kinases (RTKs) are key drivers of cancer progression and targets for drug therapy. A major challenge in anti-RTK treatment is the dependence of drug effectiveness on co-expression of multiple RTKs which defines resistance to single drug therapy. Reprogramming of the RTK network leading to alteration in RTK co-expression in response to drug intervention is a dynamic mechanism of acquired resistance to single drug therapy in many cancers. One route to overcome this resistance is combination therapy. We describe the results of a joint in silico, in vitro, and in vivo investigations on the efficacy of trastuzumab, pertuzumab and their combination to target the HER2 receptors. Computational modelling revealed that these two drugs alone and in combination differentially suppressed RTK network activation depending on RTK co-expression. Analyses of mRNA expression in SKOV3 ovarian tumour xenograft showed up-regulation of HER3 following treatment. Considering this in a computational model revealed that HER3 up-regulation reprograms RTK kinetics from HER2 homodimerisation to HER3/HER2 heterodimerisation. The results showed synergy of the trastuzumab and pertuzumab combination treatment of the HER2 overexpressing tumour can be due to an independence of the combination effect on HER3/HER2 composition when it changes due to drug-induced RTK reprogramming.
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Affiliation(s)
- Alexey Goltsov
- Scottish Informatics, Mathematics, Biology and Statistics Centre (SIMBIOS), Abertay University, Dundee, DD1 1HG, United Kingdom.
| | - Yusuf Deeni
- Scottish Informatics, Mathematics, Biology and Statistics Centre (SIMBIOS), Abertay University, Dundee, DD1 1HG, United Kingdom.
| | - Hilal S Khalil
- Scottish Informatics, Mathematics, Biology and Statistics Centre (SIMBIOS), Abertay University, Dundee, DD1 1HG, United Kingdom.
| | - Tero Soininen
- Scottish Informatics, Mathematics, Biology and Statistics Centre (SIMBIOS), Abertay University, Dundee, DD1 1HG, United Kingdom.
| | | | - Huizhong Hu
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
| | - Simon P Langdon
- Division of Pathology, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, United Kingdom.
| | - David J Harrison
- School of Medicine, University of St Andrews, St Andrews, KY16 9TF, United Kingdom.
| | - James Bown
- Scottish Informatics, Mathematics, Biology and Statistics Centre (SIMBIOS), Abertay University, Dundee, DD1 1HG, United Kingdom.
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16
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Olsen D, Jørgensen JT. Companion diagnostics for targeted cancer drugs - clinical and regulatory aspects. Front Oncol 2014; 4:105. [PMID: 24904822 PMCID: PMC4032883 DOI: 10.3389/fonc.2014.00105] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 04/28/2014] [Indexed: 01/21/2023] Open
Abstract
Companion diagnostics (CDx) holds the promise of improving the predictability of the oncology drug development process and become an important tool for the oncologist in relation to the choice of treatment for the individual patient. A number of drug-diagnostic co-development programs have already been completed successfully, and in the clinic, the use of several targeted cancer drugs is now guided by a CDx. This central role of the CDx assays has attracted the attention of the regulators, and especially the US Food and Drug Administration has been at the forefront in relation to developing regulatory strategies for CDx and the drug-diagnostic co-development project. For an increasing number of cancer patients the treatment selection will depend on the result generated by a CDx assay, and consequently this type of assay has become critical for the care and safety of the patients. In order to secure that the CDx assays have a high degree of analytical and clinical validity, they must undergo an extensive non-clinical and clinical testing before release for routine patient management. This review will give a brief introduction to some of the scientific and medical challenges related to the CDx development with specific emphasis on the regulatory requirements in different regions of the world.
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Affiliation(s)
- Dana Olsen
- Regulatory Affairs, Dako Denmark A/S, an Agilent Technologies Company , Glostrup , Denmark
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17
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Kornman KS, Polverini PJ. Clinical application of genetics to guide prevention and treatment of oral diseases. Clin Genet 2014; 86:44-9. [PMID: 24702466 PMCID: PMC4233973 DOI: 10.1111/cge.12396] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 04/03/2014] [Accepted: 04/03/2014] [Indexed: 12/13/2022]
Abstract
Dental care costs in the United States exceed $100 billion annually. Personalized medicine efforts in dentistry are driven by potentially compelling clinical utility and cost-effectiveness prospects in the major diseases of periodontitis, caries, and oral cancers. This review discusses progress and challenges identifying genetic markers and showing clinical utility in dentistry. Genome-wide association studies (GWAS) of chronic periodontitis (CP) identified no significant variants, but CDKN2BAS variants on chromosome 9 were significantly associated with aggressive periodontitis. Stratifying patients by interleukin (IL)-1 gene variants, smoking and diabetes differentiated CP prevention outcomes. Dental caries' GWAS identified significant signals in LYZL2, AJAp1, and KPNA4; and efforts are ongoing to identify genetic factors for multiple caries phenotypes. Trials of molecularly targeted therapies are in progress for oral, head, and neck squamous cell carcinomas (OHNSCC) and results have been promising but limited in their effectiveness. Current opportunities and challenges for molecular targeting for OHNSCC are discussed.
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Affiliation(s)
- K S Kornman
- Department of R&D, Interleukin Genetics, Waltham, MA, USA
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18
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Pant S, Weiner R, Marton MJ. Navigating the rapids: the development of regulated next-generation sequencing-based clinical trial assays and companion diagnostics. Front Oncol 2014; 4:78. [PMID: 24860780 PMCID: PMC4029014 DOI: 10.3389/fonc.2014.00078] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 03/28/2014] [Indexed: 12/11/2022] Open
Abstract
Over the past decade, next-generation sequencing (NGS) technology has experienced meteoric growth in the aspects of platform, technology, and supporting bioinformatics development allowing its widespread and rapid uptake in research settings. More recently, NGS-based genomic data have been exploited to better understand disease development and patient characteristics that influence response to a given therapeutic intervention. Cancer, as a disease characterized by and driven by the tumor genetic landscape, is particularly amenable to NGS-based diagnostic (Dx) approaches. NGS-based technologies are particularly well suited to studying cancer disease development, progression and emergence of resistance, all key factors in the development of next-generation cancer Dxs. Yet, to achieve the promise of NGS-based patient treatment, drug developers will need to overcome a number of operational, technical, regulatory, and strategic challenges. Here, we provide a succinct overview of the state of the clinical NGS field in terms of the available clinically targeted platforms and sequencing technologies. We discuss the various operational and practical aspects of clinical NGS testing that will facilitate or limit the uptake of such assays in routine clinical care. We examine the current strategies for analytical validation and Food and Drug Administration (FDA)-approval of NGS-based assays and ongoing efforts to standardize clinical NGS and build quality control standards for the same. The rapidly evolving companion diagnostic (CDx) landscape for NGS-based assays will be reviewed, highlighting the key areas of concern and suggesting strategies to mitigate risk. The review will conclude with a series of strategic questions that face drug developers and a discussion of the likely future course of NGS-based CDx development efforts.
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Affiliation(s)
- Saumya Pant
- Merck Research Laboratories, Molecular Biomarkers and Diagnostics , Rahway, NJ , USA
| | - Russell Weiner
- Merck Research Laboratories, Molecular Biomarkers and Diagnostics , Rahway, NJ , USA
| | - Matthew J Marton
- Merck Research Laboratories, Molecular Biomarkers and Diagnostics , Rahway, NJ , USA
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Abstract
2nd European Symposium of Biopathology Paris, France, 13-14 June, 2013 This report highlights some of the presentations and discussions at the second European Symposium of Biopathology, Paris, France, 13-14 June 2013. The symposium covered a wide range of topics in the space between molecular biology and pathology such as DNA sequencing, cancer genome interpretation, cell-free tumor DNA in plasma, molecular pathology, tissue biomarkers, biomarker discovery, companion diagnostics (CDx), drug-diagnostic co-development and targeted cancer therapy. However, in this short report, the focus will be on CDx and drug-diagnostic co-development in oncology, where a new landscape seems to emerge. As discussed at the symposium, we are slowly moving away from the 'one biomarker: one drug' scenario, which has characterized the first decades of targeted cancer drug development, toward a more integrated approach with multiple biomarkers and drugs. This 'new paradigm' will likely pave the way for the introduction of multiplexing strategies in the clinic using gene expression arrays and next-generation sequencing.
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Goltsov A, Langdon SP, Goltsov G, Harrison DJ, Bown J. Customizing the therapeutic response of signaling networks to promote antitumor responses by drug combinations. Front Oncol 2014; 4:13. [PMID: 24551596 PMCID: PMC3914444 DOI: 10.3389/fonc.2014.00013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Accepted: 01/20/2014] [Indexed: 01/26/2023] Open
Abstract
Drug resistance, de novo and acquired, pervades cellular signaling networks (SNs) from one signaling motif to another as a result of cancer progression and/or drug intervention. This resistance is one of the key determinants of efficacy in targeted anti-cancer drug therapy. Although poorly understood, drug resistance is already being addressed in combination therapy by selecting drug targets where SN sensitivity increases due to combination components or as a result of de novo or acquired mutations. Additionally, successive drug combinations have shown low resistance potential. To promote a rational, systematic development of combination therapies, it is necessary to establish the underlying mechanisms that drive the advantages of combination therapies, and design methods to determine drug targets for combination regimens. Based on a joint systems analysis of cellular SN response and its sensitivity to drug action and oncogenic mutations, we describe an in silico method to analyze the targets of drug combinations. Our method explores mechanisms of sensitizing the SN through a combination of two drugs targeting vertical signaling pathways. We propose a paradigm of SN response customization by one drug to both maximize the effect of another drug in combination and promote a robust therapeutic response against oncogenic mutations. The method was applied to customize the response of the ErbB/PI3K/PTEN/AKT pathway by combination of drugs targeting HER2 receptors and proteins in the down-stream pathway. The results of a computational experiment showed that the modification of the SN response from hyperbolic to smooth sigmoid response by manipulation of two drugs in combination leads to greater robustness in therapeutic response against oncogenic mutations determining cancer heterogeneity. The application of this method in drug combination co-development suggests a combined evaluation of inhibition effects together with the capability of drug combinations to suppress resistance mechanisms before they become clinically manifest.
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Affiliation(s)
- Alexey Goltsov
- Centre for Research in Informatics and Systems Pathology (CRISP), University of Abertay Dundee , Dundee , UK
| | - Simon P Langdon
- Division of Pathology, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh , Edinburgh , UK
| | | | | | - James Bown
- Centre for Research in Informatics and Systems Pathology (CRISP), University of Abertay Dundee , Dundee , UK
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Personalisierte Medizin. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2013; 56:1468-72. [DOI: 10.1007/s00103-013-1841-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Gremel G, Grannas K, Sutton LA, Pontén F, Zieba A. In situ Protein Detection for Companion Diagnostics. Front Oncol 2013; 3:271. [PMID: 24199171 PMCID: PMC3814083 DOI: 10.3389/fonc.2013.00271] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 10/17/2013] [Indexed: 01/29/2023] Open
Abstract
The emergence of targeted therapies for cancer has created a need for the development of companion diagnostic tests. Assays developed in recent years are aimed at determining both the effectiveness and safety of specific drugs for a defined group of patients, thus, enabling the more efficient design of clinical trials and also supporting physicians when making treatment-related decisions. Immunohistochemistry (IHC) is a widely accepted method for protein expression analyses in human tissues. Immunohistochemical assays, used to localize and quantitate relative protein expression levels within a morphological context, are frequently used as companion diagnostics during clinical trials and also following drug approval. Herein, we describe established immunochemistry-based methods and their application in routine diagnostics. We also explore the possibility of using IHC to detect specific protein mutations in addition to DNA-based tests. Finally, we review alternative protein binders and proximity ligation assays and discuss their potential to facilitate the development of novel, targeted therapies against cancer.
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Affiliation(s)
- Gabriela Gremel
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University , Uppsala , Sweden
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