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Feilotter H, Bruce C, Diamandis EP, Chatanaka MK, Yousef GM. Guidance for securing approvals for new biomarkers: from discovery to clinical implementation. Crit Rev Clin Lab Sci 2024:1-8. [PMID: 39084247 DOI: 10.1080/10408363.2024.2379278] [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: 05/10/2024] [Revised: 06/04/2024] [Accepted: 07/09/2024] [Indexed: 08/02/2024]
Abstract
The journey of translating a molecular discovery into the clinic involves multiple steps and requires planning, time, effort, and money. In this review, we provide a quick guide on the technical and clinical validation parameters that are necessary for successful commercialization of molecular and other markers. We also briefly address the different options for regulatory approvals. Successful clinical implantation depends on rigorous technical and clinical validation, and the ability to develop clear guidelines for the indications for testing (i.e. which patients are eligible to have this test), the frequency of testing, and also a clear interpretation of test results. Successful implementation requires providing evidence that the results of this test can be used to improve patient care. There are currently multiple routes for implementation of clinical molecular tests, which include regulatory agency- approved companion diagnostics, laboratory developed tests, or direct-to-consumer testing. Regulatory approval is considered the gold-standard, but it requires time and resources. There is an ongoing debate about the need for regulatory approval of laboratory developed testing. Ongoing oversight is maintained through lab accreditation and proficiency testing programs, which provide a common approach to ensuring high standards and consistent performance in clinical molecular labs. Before moving into the clinic, confirmation of both the clinical and analytic validity of a new molecular test is essential.
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Affiliation(s)
- Harriet Feilotter
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Christine Bruce
- Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Eleftherios P Diamandis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, Canada
| | - Miyo K Chatanaka
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - George M Yousef
- Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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2
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Khatab Z, Hanna K, Rofaeil A, Wang C, Maung R, Yousef GM. Pathologist workload, burnout, and wellness: connecting the dots. Crit Rev Clin Lab Sci 2024; 61:254-274. [PMID: 38809116 DOI: 10.1080/10408363.2023.2285284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 11/15/2023] [Indexed: 05/30/2024]
Abstract
No standard tool to measure pathologist workload currently exists. An accurate measure of workload is needed for determining the number of pathologists to be hired, distributing the workload fairly among pathologists, and assessing the overall cost of pathology consults. Initially, simple tools such as counting cases or slides were used to give an estimate of the workload. More recently, multiple workload models, including relative value units (RVUs), the Royal College of Pathologists (RCP) point system, Level 4 Equivalent (L4E), Work2Quality (W2Q), and the University of Washington, Seattle (UW) slide count method, have been developed. There is no "ideal" model that is universally accepted. The main differences among the models come from the weights assigned to different specimen types, differential calculations for organs, and the capture of additional tasks needed for safe and timely patient care. Academic centers tend to see more complex cases that require extensive sampling and additional testing, while community-based and private laboratories deal more with biopsies. Additionally, some systems do not account for teaching, participation in multidisciplinary rounds, quality assurance activities, and medical oversight. A successful workload model needs to be continually updated to reflect the current state of practice.Awareness about physician burnout has gained attention in recent years and has been added to the World Health Organization's International Classification of Diseases (World Health Organization, WHO) as an occupational phenomenon. However, the extent to which this affects pathologists is not well understood. According to the WHO, burnout syndrome is diagnosed by the presence of three components: emotional exhaustion, depersonalization from one's work (cynicism related to one's job), and a low sense of personal achievement or accomplishment. Three drivers of burnout are the demand for productivity, lack of recognition, and electronic health records. Prominent consequences of physician burnout are economic and personal costs to the public and to the providers.Wellness is physical and mental well-being that allows individuals to manage stress effectively and to thrive in both their professional and personal lives. To achieve wellness, it is necessary to understand the root causes of burnout, including over-work and working under stressful conditions. Wellness is more than the absence of stress or burnout, and the responsibility of wellness should be shared by pathologists themselves, their healthcare organization, and governing bodies. Each pathologist needs to take their own path to achieve wellness.
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Affiliation(s)
- Ziyad Khatab
- Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Kattreen Hanna
- Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Andrew Rofaeil
- Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Catherine Wang
- Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Raymond Maung
- University Hospital of Northern British Columbia, Prince George, BC, Canada
| | - George M Yousef
- Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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3
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McKenna DB, Sanchez P, Powers J, Brower J, Wang L, Mueller R, Symecko H, Hamilton JG, Wildman T, Domchek SM, Couch FJ, Garber JE, Offit K, Robson ME, Katona BW. Summary of the experiences, knowledge, medical management, and family communication of monoallelic MUTYH carriers. J Genet Couns 2023; 32:342-350. [PMID: 36245263 PMCID: PMC10436665 DOI: 10.1002/jgc4.1641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 11/10/2022]
Abstract
Germline genetic testing for inherited cancer risk is increasingly being performed with multigene panel testing with MUTYH often included on colorectal cancer- and polyposis-focused panels, as well as on broader pan-cancer panels. With up to 1%-2% of the general population being monoallelic MUTYH carriers, pathogenic/likely pathogenic (P/LP) variants in MUTYH are one of the most common findings on multigene cancer panels. However, little is known about patient experience and understanding of monoallelic MUTYH P/LP variants, nor whether such findings influence medical management recommendations and familial communication, which this study aims to better understand. Monoallelic P/LP MUTYH carriers were recruited from the Prospective Registry of Multiplex Testing (PROMPT) and completed a cross-sectional self-report survey on sociodemographic characteristics, medical and family history, experiences with MUTYH genetic testing, genetics and MUTYH knowledge, perceived cancer risk, and familial communication. Of 115 eligible PROMPT participants, 49 (43%) completed the survey who were primarily female (94%), white (96%), had a history of cancer (61%), and a median age of 51.4 years. Most participants (61%) reported satisfaction with how their healthcare provider managed their genetic test result and care, and 65% of survey participants reported their provider recommended colonoscopy based on their genetic test results. Participants' responses also reflected variable levels of knowledge regarding cancer risks and screening recommendations for MUTYH carriers. The majority (98%) of participants shared their genetic test results with at least some of their relatives; however, only 13% of eligible relatives reportedly underwent cascade testing. Taken together, this study provides needed insight into the overall experiences of monoallelic MUTYH carriers and highlights numerous areas for improvement in clinician education, communication, and management of these individuals.
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Affiliation(s)
- Danielle B. McKenna
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Pauleen Sanchez
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jacquelyn Powers
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jamie Brower
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Louise Wang
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Rebecca Mueller
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Heather Symecko
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jada G. Hamilton
- Department of Psychiatry & Behavioral Sciences, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Weill Cornell Medical College, New York, New York, USA
| | - Temima Wildman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Susan M. Domchek
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Judy E. Garber
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Weill Cornell Medical College, New York, New York, USA
| | - Mark E. Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Weill Cornell Medical College, New York, New York, USA
| | - Bryson W. Katona
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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4
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Tommel J, Kenis D, Lambrechts N, Brohet RM, Swysen J, Mollen L, Hoefmans MJF, Pusparum M, Evers AWM, Ertaylan G, Roos M, Hens K, Houwink EJF. Personal Genomes in Practice: Exploring Citizen and Healthcare Professionals' Perspectives on Personalized Genomic Medicine and Personal Health Data Spaces Using a Mixed-Methods Design. Genes (Basel) 2023; 14:786. [PMID: 37107544 PMCID: PMC10137790 DOI: 10.3390/genes14040786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/15/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023] Open
Abstract
Ongoing health challenges, such as the increased global burden of chronic disease, are increasingly answered by calls for personalized approaches to healthcare. Genomic medicine, a vital component of these personalization strategies, is applied in risk assessment, prevention, prognostication, and therapeutic targeting. However, several practical, ethical, and technological challenges remain. Across Europe, Personal Health Data Space (PHDS) projects are under development aiming to establish patient-centered, interoperable data ecosystems balancing data access, control, and use for individual citizens to complement the research and commercial focus of the European Health Data Space provisions. The current study explores healthcare users' and health care professionals' perspectives on personalized genomic medicine and PHDS solutions, in casu the Personal Genetic Locker (PGL). A mixed-methods design was used, including surveys, interviews, and focus groups. Several meta-themes were generated from the data: (i) participants were interested in genomic information; (ii) participants valued data control, robust infrastructure, and sharing data with non-commercial stakeholders; (iii) autonomy was a central concern for all participants; (iv) institutional and interpersonal trust were highly significant for genomic medicine; and (v) participants encouraged the implementation of PHDSs since PHDSs were thought to promote the use of genomic data and enhance patients' control over their data. To conclude, we formulated several facilitators to implement genomic medicine in healthcare based on the perspectives of a diverse set of stakeholders.
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Affiliation(s)
- Judith Tommel
- Health, Medical, and Neuropsychology Unit, Institute of Psychology, Faculty of Social and Behavioural Sciences, Leiden University, Wassenaarseweg 52, 2333 AK Leiden, The Netherlands
- Department of Psychiatry, University of Groningen, University Medical Centre Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Daan Kenis
- Department of Philosophy, University of Antwerp, Rodestraat 14, 2000 Antwerp, Belgium
| | | | - Richard M. Brohet
- Department of Epidemiology and Statistics, Isala Hospital, Dokter van Heesweg 2, 8025 AB Zwolle, The Netherlands
| | | | | | | | - Murih Pusparum
- VITO Health, Boeretang 200, 2400 Mol, Belgium
- Data Science Institute, I-Biostat, Hasselt University, 3500 Hasselt, Belgium
| | - Andrea W. M. Evers
- Health, Medical, and Neuropsychology Unit, Institute of Psychology, Faculty of Social and Behavioural Sciences, Leiden University, Wassenaarseweg 52, 2333 AK Leiden, The Netherlands
| | | | - Marco Roos
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Kristien Hens
- Department of Philosophy, University of Antwerp, Rodestraat 14, 2000 Antwerp, Belgium
| | - Elisa J. F. Houwink
- Department of Family Medicine, Mayo Clinic, 221 Fourth Avenue SW, Rochester, MN 55905, USA
- Department of Public Health and Primary Care (PHEG), Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
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5
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Semen as a rich source of diagnostic biomarkers for prostate cancer: latest evidence and implications. Mol Cell Biochem 2021; 477:213-223. [PMID: 34655417 DOI: 10.1007/s11010-021-04273-4] [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: 05/11/2021] [Accepted: 10/01/2021] [Indexed: 12/24/2022]
Abstract
Prostate cancer (PCa) is one of the most common cancers in men and the cause of numerous cancer deaths in the world. Nowadays, based on diagnostic criteria, prostate-specific antigen (PSA) evaluation and rectal examination are used to diagnose prostate-related malignancies. However, due to the different types of PCa, there are several doubts about the diagnostic value of PSA. On the other hand, semen is considered an appropriate source and contains various biomarkers in non-invasive diagnosing several autoimmune disorders and malignancies. Evidence suggests that analysis of semen biomarkers could be helpful in PCa diagnosis. Therefore, due to the invasiveness of most diagnostic methods in PCa, the use of semen as a biologic sample containing various biomarkers can lead to the emergence of novel and non-invasive diagnostic approaches. This review summarized recent studies on the use of various seminal biomarkers for diagnosis, prognosis and prediction of PCa.
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Abstract
OBJECTIVES The pathology report serves as a crucial communication tool among a number of stakeholders. It can sometimes be challenging to understand. A communication barrier exists among pathologists, other clinicians, and patients when interpreting the pathology report, leaving both clinicians and patients less empowered when making treatment decisions. Miscommunication can lead to delays in treatment or other costly medical interventions. METHODS In this review, we highlight miscommunication in pathology reporting and provide potential solutions to improve communication. RESULTS Up to one-third of clinicians do not always understand pathology reports. Several causes of report misinterpretation include the use of pathology-specific jargon, different versions of staging or grading systems, and expressions indicative of uncertainty in the pathologist's report. Active communication has proven to be crucial between the clinician and the pathologist to clarify different aspects of the pathology report. Direct communication between pathologists and patients is evolving, with promising success in proof-of-principle studies. Special attention needs to be paid to avoiding inaccuracy while trying to simplify the pathology report. CONCLUSIONS There is a need for active and adequate communication among pathologists, other clinicians, and patients. Clarity and consistency in reporting, quantifying the level of confidence in diagnosis, and avoiding misnomers are key steps toward improving communications.
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Affiliation(s)
- Lorna Mirham
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Laboratory Medicine, North York General Hospital, Toronto, Canada
| | - Jessica Hanna
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada
| | - George M Yousef
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Paediatric Laboratory Medicine, the Hospital for Sick Children, Toronto, Canada
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7
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Khatab Z, Yousef GM. Disruptive innovations in the clinical laboratory: catching the wave of precision diagnostics. Crit Rev Clin Lab Sci 2021; 58:546-562. [PMID: 34297653 DOI: 10.1080/10408363.2021.1943302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Disruptive innovation is an invention that disrupts an existing market and creates a new one by providing a different set of values, which ultimately overtakes the existing market. Typically, when disruptive innovations are introduced, their performance is initially less than existing standard technologies, but because of their ability to bring the cost down, and with gradual improvement, they end up replacing established service standards.Disruptive technologies have their fingerprints in health care. Pathology and laboratory medicine are fertile soils for disruptive innovations because they are heavily reliant on technology. Disruptive innovations have resulted in a revolution of our diagnostic ability and will take laboratory medicine to the next level of patient care. There are several examples of disruptive innovations in the clinical laboratory. Digitizing pathology practice is an example of disruptive technology, with many advantages and an extended scope of applications. Next-generation sequencing can be disruptive in two ways. The first is by replacing an array of laboratory tests, which each requires expensive and specialized instruments and expertise, with a single cost-effective technology. The second is by disrupting the current paradigm of the clinical laboratory as a diagnostic service by taking it into a new era of preventive or primary care pathology. Other disruptive innovations include the use of dry chemistry reagents in chemistry analyzers and also point of care testing. The use of artificial intelligence is another promising disruptive innovation that can transform the future of pathology and laboratory medicine. Another emerging disruptive concept is the integration of two fields of medicine to create an interrelated discipline such as "histogenomics and radiohistomics." Another recent disruptive innovation in laboratory medicine is the use of social media in clinical practice, education, and publication.There are multiple reasons to encourage disruptive innovations in the clinical laboratory, including the escalating cost of health care, the need for better accessibility of diagnostic care, and the increased demand on the laboratory in the era of precision diagnostics. There are, however, a number of challenges that need to be overcome such as the significant resistance to disruptive innovations by current technology providers and governmental regulatory bodies. The hesitance from health care providers and insurance companies must also be addressed.Adoption of disruptive innovations requires a multifaceted approach that involves orchestrated solutions to key aspects of the process, including creating successful business models, multidisciplinary collaborations, and innovative accreditation and regulatory oversight. It also must be coupled with successful commercialization plans and modernization of health care structure. Fostering a culture of disruptive innovation requires establishing unique collaborative models between academia and industry. It also requires uncovering new sources of unconventional funding that are open to high-risk high-reward projects. It should also be matched with innovative thinking, including new approaches for delivery of care and identifying novel cohorts of patients who can benefit from disruptive technology.
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Affiliation(s)
- Ziyad Khatab
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - George M Yousef
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
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8
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Urine as a Source of Liquid Biopsy for Cancer. Cancers (Basel) 2021; 13:cancers13112652. [PMID: 34071230 PMCID: PMC8199052 DOI: 10.3390/cancers13112652] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/20/2021] [Accepted: 05/25/2021] [Indexed: 12/18/2022] Open
Abstract
Simple Summary Tissue biopsy is essential for diagnosis and characterization of a tumor. Recently circulating tumor cells and other tumor-derived nucleic acid can be detected from blood, which is called liquid biopsy. Now this concept has been expanded to many other body fluids including urine. Urine is the least invasive method to obtain a liquid biopsy and can be done anywhere, which allows longitudinal repeated sampling. Here, we review the latest update on urine liquid biopsy in urological and non-urological cancers. Abstract Tissue biopsy is the gold standard for diagnosis and morphological and immunohistochemical analyses to characterize cancer. However, tissue biopsy usually requires an invasive procedure, and it can be challenging depending on the condition of the patient and the location of the tumor. Even liquid biopsy analysis of body fluids such as blood, saliva, gastric juice, sweat, tears and cerebrospinal fluid may require invasive procedures to obtain samples. Liquid biopsy can be applied to circulating tumor cells (CTCs) or nucleic acids (NAs) in blood. Recently, urine has gained popularity due to its less invasive sampling, ability to easily repeat samples, and ability to follow tumor evolution in real-time, making it a powerful tool for diagnosis and treatment monitoring in cancer patients. With the development and advancements in extraction methods of urinary substances, urinary NAs have been found to be closely related to carcinogenesis, metastasis, and therapeutic response, not only in urological cancers but also in non-urological cancers. This review mainly highlights the components of urine liquid biopsy and their utility and limitations in oncology, especially in non-urological cancers.
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9
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Carress H, Lawson DJ, Elhaik E. Population genetic considerations for using biobanks as international resources in the pandemic era and beyond. BMC Genomics 2021; 22:351. [PMID: 34001009 PMCID: PMC8127217 DOI: 10.1186/s12864-021-07618-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 04/14/2021] [Indexed: 12/11/2022] Open
Abstract
The past years have seen the rise of genomic biobanks and mega-scale meta-analysis of genomic data, which promises to reveal the genetic underpinnings of health and disease. However, the over-representation of Europeans in genomic studies not only limits the global understanding of disease risk but also inhibits viable research into the genomic differences between carriers and patients. Whilst the community has agreed that more diverse samples are required, it is not enough to blindly increase diversity; the diversity must be quantified, compared and annotated to lead to insight. Genetic annotations from separate biobanks need to be comparable and computable and to operate without access to raw data due to privacy concerns. Comparability is key both for regular research and to allow international comparison in response to pandemics. Here, we evaluate the appropriateness of the most common genomic tools used to depict population structure in a standardized and comparable manner. The end goal is to reduce the effects of confounding and learn from genuine variation in genetic effects on phenotypes across populations, which will improve the value of biobanks (locally and internationally), increase the accuracy of association analyses and inform developmental efforts.
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Affiliation(s)
- Hannah Carress
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Daniel John Lawson
- School of Mathematics and Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Eran Elhaik
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK. .,Department of Biology, Lund University, Lund, Sweden.
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10
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Cimmino I, Bravaccini S, Cerchione C. Urinary Biomarkers in Tumors: An Overview. Methods Mol Biol 2021; 2292:3-15. [PMID: 33651347 DOI: 10.1007/978-1-0716-1354-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Recent reports suggest that urine is a useful noninvasive tool for the identification of urogenital tumors, including bladder, prostate, kidney, and other nonurological cancers. As a liquid biopsy, urine represents an important source for the improvement of new promising biomarkers, a suitable tool to identify indolent cancer and avoid overtreatment. Urine is enriched with DNAs, RNAs, proteins, circulating tumor cells, exosomes, and other small molecules which can be detected with several diagnostic methodologies.We provide an overview of the ongoing state of urinary biomarkers underlying both their potential utilities to improve cancer prognosis, diagnosis, and therapeutic strategy and their limitations.
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Affiliation(s)
- Ilaria Cimmino
- Department of Translational Medicine, University of Naples "Federico II", Naples, Italy
| | - Sara Bravaccini
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Claudio Cerchione
- Hematology Unit, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy.
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11
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Donohue KE, Gooch C, Katz A, Wakelee J, Slavotinek A, Korf BR. Pitfalls and challenges in genetic test interpretation: An exploration of genetic professionals experience with interpretation of results. Clin Genet 2021; 99:638-649. [PMID: 33818754 DOI: 10.1111/cge.13917] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/11/2020] [Accepted: 01/04/2021] [Indexed: 12/17/2022]
Abstract
The interpretation of genetic testing results is subject to error. This observational study illustrates examples of pitfalls and challenges in interpretation of genetic testing results as reported by genetics professionals. We surveyed genetics professionals to describe interpretation challenges, the types of variants that were involved, and the reported clinical impact of misconception of a test result. Case studies were then collected from a select group to further explore potential causes of misunderstanding. A total of 83% of survey respondents were aware of at least one instance of genetic test misinterpretation. Both professionals with and without formal training in genetics were challenged by test reports, and variants of unknown significance were most frequently involved. Case submissions revealed that interpretation pitfalls extend beyond variant classification analyses. Inferred challenges in case submissions include lack of genetic counseling, unclear wording of reports, and suboptimal communication among providers. Respondents and case submitters noted that incorrect interpretation can trigger unnecessary follow-up tests and improperly alter clinical management. Further research is needed to validate and quantify large-scale data regarding challenges of genetic results interpretation.
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Affiliation(s)
- Katherine E Donohue
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Catherine Gooch
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Pediatrics, Division of Genetics and Genomic Medicine, Washington University at St Louis School of Medicine, St. Louis, MO, USA
| | - Alexander Katz
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Jessica Wakelee
- Center for the Study of Community Health, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Anne Slavotinek
- Division of Genetics, Department of Pediatrics, University of California, San Francisco, California, USA
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
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12
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Transcriptome analysis of arterial and venous circulating miRNAs during hypertension. Sci Rep 2021; 11:3469. [PMID: 33568719 PMCID: PMC7875986 DOI: 10.1038/s41598-021-82979-7] [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: 03/25/2020] [Accepted: 01/04/2021] [Indexed: 11/18/2022] Open
Abstract
Most current circulating miRNA biomarkers are derived from peripheral venous blood, whereas miRNA deregulation in arterial blood in disease conditions has been largely ignored. To explore whether peripheral venous blood miRNAs could represent a bona fide specific miRNA deregulation pattern, we selected hypertension, a disease that is particularly associated with vessels, as the model. Circulating miRNA profiles of arterial and venous blood from spontaneously hypertensive (SHR) rats and their corresponding controls (i.e., WKY rats) were investigated by next-generation miRNA sequencing. Little miRNAs were observed between arterial and venous circulating miRNAs in WKY rats. Interestingly, this number was enhanced in SHR hypertensive rats. Bioinformatical analysis of disease association, enriched target genes and the regulatory transcription factors of these differentially expressed miRNAs implied a potential functional link with cardiovascular disease-related functions. Comparisons between arterial and venous miRNAs in hypertension-versus-control conditions also revealed prominent disease association of circulating miRNAs and their target genes in arteries but not in veins. Moreover, a young non-hypertensive animal model in SHR background (i.e. JSHR) was used as a second control for SHR. Additional transcriptomic analysis and droplet digital PCR validation of arterial and venous deregulated miRNAs among SHR and its two controls (WKY, JSHR) revealed a noticeable consensus of artery-deregulated miRNAs in hypertension and two novel arterial circulating signatures (miR-455-3p and miR-140-3p) of hypertension. These results suggest the necessity of re-evaluating the efficacy of certain venous miRNAs identified in previous studies as potential biomarkers in cardiovascular diseases or a wider disease spectrum.
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13
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Liu W, Ju L, Cheng S, Wang G, Qian K, Liu X, Xiao Y, Wang X. Conditional reprogramming: Modeling urological cancer and translation to clinics. Clin Transl Med 2020; 10:e95. [PMID: 32508060 PMCID: PMC7403683 DOI: 10.1002/ctm2.95] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 12/12/2022] Open
Abstract
Patient-derived models, including cell models (organoids and conditionally reprogrammed cells [CRCs]) and patient-derived xenografts, are urgently needed for both basic and translational cancer research. Conditional reprogramming (CR) technique refers to a co-culture system of primary human normal or tumor cells with irradiated murine fibroblasts in the presence of a Rho-associated kinase inhibitor to allow the primary cells to acquire stem cell properties and the ability to proliferate indefinitely in vitro without any exogenous gene or viral transfection. Considering its robust features, the CR technique may facilitate cancer research in many aspects. Under in vitro culturing, malignant CRCs can share certain genetic aberrations and tumor phenotypes with their parental specimens. Thus, tumor CRCs can promisingly be utilized for the study of cancer biology, the discovery of novel therapies, and the promotion of precision medicine. For normal CRCs, the characteristics of normal karyotype maintenance and lineage commitment suggest their potential in toxicity testing and regenerative medicine. In this review, we discuss the applications, limitations, and future potential of CRCs in modeling urological cancer and translation to clinics.
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Affiliation(s)
- Wei Liu
- Department of UrologyZhongnan Hospital of Wuhan UniversityWuhanChina
| | - Lingao Ju
- Department of Biological RepositoriesZhongnan Hospital of Wuhan UniversityWuhanChina
- Human Genetic Resources Preservation Center of Hubei ProvinceWuhanChina
| | - Songtao Cheng
- Department of UrologyZhongnan Hospital of Wuhan UniversityWuhanChina
| | - Gang Wang
- Department of Biological RepositoriesZhongnan Hospital of Wuhan UniversityWuhanChina
- Human Genetic Resources Preservation Center of Hubei ProvinceWuhanChina
| | - Kaiyu Qian
- Department of Biological RepositoriesZhongnan Hospital of Wuhan UniversityWuhanChina
- Human Genetic Resources Preservation Center of Hubei ProvinceWuhanChina
| | - Xuefeng Liu
- Department of Pathology, Lombardi Comprehensive Cancer CenterGeorgetown University Medical CenterWashingtonDC
| | - Yu Xiao
- Department of UrologyZhongnan Hospital of Wuhan UniversityWuhanChina
- Department of Biological RepositoriesZhongnan Hospital of Wuhan UniversityWuhanChina
- Human Genetic Resources Preservation Center of Hubei ProvinceWuhanChina
| | - Xinghuan Wang
- Department of UrologyZhongnan Hospital of Wuhan UniversityWuhanChina
- Medical Research InstituteWuhan UniversityWuhanChina
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14
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Barsoum I, Tawedrous E, Faragalla H, Yousef GM. Histo-genomics: digital pathology at the forefront of precision medicine. ACTA ACUST UNITED AC 2020; 6:203-212. [PMID: 30827078 DOI: 10.1515/dx-2018-0064] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/28/2018] [Indexed: 12/26/2022]
Abstract
The toughest challenge OMICs face is that they provide extremely high molecular resolution but poor spatial information. Understanding the cellular/histological context of the overwhelming genetic data is critical for a full understanding of the clinical behavior of a malignant tumor. Digital pathology can add an extra layer of information to help visualize in a spatial and microenvironmental context the molecular information of cancer. Thus, histo-genomics provide a unique chance for data integration. In the era of a precision medicine, a four-dimensional (4D) (temporal/spatial) analysis of cancer aided by digital pathology can be a critical step to understand the evolution/progression of different cancers and consequently tailor individual treatment plans. For instance, the integration of molecular biomarkers expression into a three-dimensional (3D) image of a digitally scanned tumor can offer a better understanding of its subtype, behavior, host immune response and prognosis. Using advanced digital image analysis, a larger spectrum of parameters can be analyzed as potential predictors of clinical behavior. Correlation between morphological features and host immune response can be also performed with therapeutic implications. Radio-histomics, or the interface of radiological images and histology is another emerging exciting field which encompasses the integration of radiological imaging with digital pathological images, genomics, and clinical data to portray a more holistic approach to understating and treating disease. These advances in digital slide scanning are not without technical challenges, which will be addressed carefully in this review with quick peek at its future.
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Affiliation(s)
- Ivraym Barsoum
- Department of Pathology and Molecular Medicine, Faculty of Health Sciences, Queen's University, Kingston, Ontario, Canada
| | - Eriny Tawedrous
- Department of Laboratory Medicine, and the Keenan Research Centre for Biomedical Science at the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
| | - Hala Faragalla
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - George M Yousef
- Department of Laboratory Medicine, and the Keenan Research Centre for Biomedical Science at the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada
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15
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Morgan S, Hanna J, Yousef GM. Knowledge Translation in Oncology: The Bumpy Ride From Bench to Bedside. Am J Clin Pathol 2020; 153:5-13. [PMID: 31836881 DOI: 10.1093/ajcp/aqz099] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES Knowledge translation (KT) is the dynamic process of mobilizing best-practice evidence to guide health care decisions. METHODS Using a PubMed search, challenges were identified and milestones defined. RESULTS Substantial challenges exist in integrating discoveries into patient care, including technical limitations related to genomic testing like turnaround time, standardization, reproducibility, and results interpretation. Other challenges include lack of proper training in genetic counseling for health care providers, clarity of scientific evidence, and ethical, legal and social considerations. In addition, most health care systems lack accessibility to genetic testing services. Moving forward, KT should be addressed at three main frontiers. The first is patients centered for proper understanding and decision making; the second is directed toward health care professionals, including clinical decision support and clarity of roles; and the third addresses resources of health care systems. CONCLUSIONS Implementing KT requires developing strategies to enhance awareness and promote behavioral changes congruent with research evidence, designing a systematic approach by health care providers and stakeholders to achieve patient-centered care.
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Affiliation(s)
- Sarah Morgan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Canada
| | - Jessica Hanna
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Canada
| | - George M Yousef
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Canada
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16
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Del Re M, Crucitta S, Gianfilippo G, Passaro A, Petrini I, Restante G, Michelucci A, Fogli S, de Marinis F, Porta C, Chella A, Danesi R. Understanding the Mechanisms of Resistance in EGFR-Positive NSCLC: From Tissue to Liquid Biopsy to Guide Treatment Strategy. Int J Mol Sci 2019; 20:ijms20163951. [PMID: 31416192 PMCID: PMC6720634 DOI: 10.3390/ijms20163951] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/07/2019] [Accepted: 08/09/2019] [Indexed: 02/06/2023] Open
Abstract
Liquid biopsy has emerged as an alternative source of nucleic acids for the management of Epidermal Growth Factor Receptor (EGFR)-mutant non-Small Cell Lung Cancer (NSCLC). The use of circulating cell-free DNA (cfDNA) has been recently introduced in clinical practice, resulting in the improvement of the identification of druggable EGFR mutations for the diagnosis and monitoring of response to targeted therapy. EGFR-dependent (T790M and C797S mutations) and independent (Mesenchymal Epithelial Transition [MET] gene amplification, Kirsten Rat Sarcoma [KRAS], Phosphatidyl-Inositol 4,5-bisphosphate 3-Kinase Catalytic subunit Alpha isoform [PI3KCA], and RAF murine sarcoma viral oncogene homolog B1 [BRAF] gene mutations) mechanisms of resistance to EGFR tyrosine kinase inhibitors (TKIs) have been evaluated in plasma samples from NSCLC patients using highly sensitive methods (i.e., digital droplet PCR, Next Generation Sequencing), allowing for the switch to other therapies. Therefore, liquid biopsy is a non-invasive method able to detect the molecular dynamic changes that occur under the pressure of treatment, and to capture tumor heterogeneity more efficiently than is allowed by tissue biopsy. This review addresses how liquid biopsy may be used to guide the choice of treatment strategy in EGFR-mutant NSCLC.
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Affiliation(s)
- Marzia Del Re
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy.
| | - Stefania Crucitta
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
| | - Giulia Gianfilippo
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
| | - Antonio Passaro
- Division of Thoracic Oncology, European Institute of Oncology, 20141 Milano, Italy
| | - Iacopo Petrini
- General Pathology, Department of Translational Research & New Technologies in Surgery and Medicine, University of Pisa, 56126 Pisa, Italy
| | - Giuliana Restante
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
| | - Angela Michelucci
- Unit of Molecular Genetics, Department of Laboratory Medicine, University Hospital, 56126 Pisa, Italy
| | - Stefano Fogli
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
| | - Filippo de Marinis
- Division of Thoracic Oncology, European Institute of Oncology, 20141 Milano, Italy
| | - Camillo Porta
- Department of Internal Medicine, University of Pavia, 27100 Pavia, Italy
- Division of Translational Oncology, I.R.C.C.S. Istituti Clinici Scientifici Maugeri, 27100 Pavia, Italy
| | - Antonio Chella
- Unit of Respiratory Medicine, Department of Critical Area and Surgical, Medical and Molecular Pathology, University Hospital, 56126 Pisa, Italy
| | - Romano Danesi
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
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17
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Oliveri S, Mainetti R, Gorini A, Cutica I, Candiani G, Borghese NA, Pravettoni G. Serious Games for Improving Genetic Literacy and Genetic Risk Awareness in the General Public: Protocol for a Randomized Controlled Trial. JMIR Res Protoc 2018; 7:e189. [PMID: 30563813 PMCID: PMC6315238 DOI: 10.2196/resprot.9288] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 06/04/2018] [Accepted: 07/16/2018] [Indexed: 12/13/2022] Open
Abstract
Background Genetic testing and genetic risk information are gaining importance in personalized medicine and disease prevention. However, progress in these fields does not reflect increased knowledge and awareness of genetic risk in the general public. Objective Our aim is to develop and test the efficacy of a suite of serious games, developed for mobile and Web platforms, in order to increase knowledge of basic genetic concepts and promote awareness of genetic risk management among lay people. Methods We developed a new ad-hoc game and modified an arcade game using mechanics suitable to explain genetic concepts. In addition, we developed an adventure game where players are immersed in virtual scenarios and manage genetic risk information to make health-related and interpersonal decisions and modulate their lifestyle. The pilot usability testing will be conducted with a convenience sample of 30 adults who will be categorized into 3 groups and assigned to one game each. Participants will be asked to report any positive or negative issues arising during the game. Subsequently, they will be asked to complete the Game Experience Questionnaire. Finally, a total of 60 teenagers and adults will be enrolled to assess knowledge transfer. Thirty participants will be assigned to the experimental group and asked to play the serious games, and 30 participants will be assigned to the control group and asked to read leaflets on the genetic concepts conveyed by the games. Participants of both groups will fill out a questionnaire before and after the intervention to assess their topic-specific knowledge of genetics. Furthermore, both groups will complete the self-efficacy questionnaire, which assesses the level of confidence in using genetic information. Results We obtained evidence of game usability in 2017. The data will be submitted to a peer-reviewed journal and used to improve the game design. Knowledge-transfer testing will begin in 2018, and we expect to collect preliminary data on the learning outcomes of serious games by December 2018. Conclusions It is important to educate the general public about the impact of genetics and genetic testing on disease prevention and the consequent decision-making implications. Without such knowledge, individuals are more likely to make uninformed decisions or handover all decisions regarding genetic testing to their doctors. Technological innovations such as serious games might become a valid instrument to support public education and empowerment. International Registered Report Identifier (IRRID) DERR1-10.2196/9288
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Affiliation(s)
- Serena Oliveri
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
| | - Renato Mainetti
- Applied Intelligent Systems Laboratory, Department of Computer Science, Università degli Studi di Milano, Milan, Italy
| | - Alessandra Gorini
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
| | - Ilaria Cutica
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
| | | | - Nunzio Alberto Borghese
- Applied Intelligent Systems Laboratory, Department of Computer Science, Università degli Studi di Milano, Milan, Italy
| | - Gabriella Pravettoni
- Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan, Italy
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18
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Khella HWZ, Yousef GM. Translational research: Empowering the role of pathologists and cytopathologists. Cancer Cytopathol 2018; 126:831-838. [PMID: 30281935 DOI: 10.1002/cncy.22046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 07/13/2018] [Accepted: 07/16/2018] [Indexed: 12/17/2022]
Abstract
Research activity is in the core essence of pathology. Advancing our understanding of disease pathogenesis translates into better patient care. Because of their unique position, laboratorians are the best to accurately identify, annotate, and classify research specimens. They also are essential for the accurate interpretation of genomic testing. Currently, cytopathologists are moving to the center of patient care through active communication with clinicians and patients. There are certain research areas in which cytopathologists can be pioneers, such as image analysis, morphology research, and genotype-phenotype association studies integrating morphologic and molecular features. Health service utilization research is another domain in which cytopathologists can excel. Successful research is a journey that necessitates multiple steps. It also involves building expertise in how to overcome obstacles and handle challenges.
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Affiliation(s)
- Heba W Z Khella
- Department of Laboratory Medicine, Keenan Research Center at the Li Ka Shing Knowledge Institute of St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Anatomy, Canadian Memorial Chiropractic College, North York, Ontario, Canada
| | - George M Yousef
- Department of Laboratory Medicine, Keenan Research Center at the Li Ka Shing Knowledge Institute of St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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19
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Helm BM, Ayers MD, Kean AC. All Along the Watchtower: a Case of Long QT Syndrome Misdiagnosis Secondary to Genetic Testing Misinterpretation. J Genet Couns 2018; 27:1515-1522. [DOI: 10.1007/s10897-018-0287-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 08/02/2018] [Indexed: 11/29/2022]
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20
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Arneth B. Update on the types and usage of liquid biopsies in the clinical setting: a systematic review. BMC Cancer 2018; 18:527. [PMID: 29728089 PMCID: PMC5935950 DOI: 10.1186/s12885-018-4433-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 04/25/2018] [Indexed: 12/23/2022] Open
Abstract
Background This systematic review aimed to gather evidence from research on the current state of liquid biopsy in medical practice, specifically focusing on mutation detection and monitoring. Methods A systematic search was performed via Medline. Results The results of this investigation indicate that liquid biopsy plays a critical role in the detection and management of tumors. This technique gives healthcare providers the ability to gather critical and reliable information that may potentially shape the diagnosis, treatment, and prognosis of a variety of cancers in the near future. This study further reveals that liquid biopsy has several potential shortcomings that may limit its application and use in the healthcare setting. Nevertheless, liquid biopsy remains a valuable tool that is gradually becoming a part of routine healthcare practice in oncology departments and hospitals worldwide. Conclusions The evidence described herein reveals the potential relevance of liquid biopsy as an important prognostic, diagnostic, and theranostic tool. This non-invasive procedure enables healthcare practitioners to detect and monitor genomic alterations and will likely replace tumor tissue biopsy as the standard method for detecting and monitoring mutations in the future. The information obtained herein can enable physicians to make informed decisions regarding current treatment options; however, liquid biopsy has not yet been incorporated into routine clinical diagnostics for cancer patients.
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Affiliation(s)
- Borros Arneth
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, University Hospital of the Universities of Giessen and Marburg UKGM, Justus Liebig University Giessen, Feulgenstr. 12, 35392, Giessen, Germany.
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21
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Di Meo A, Bartlett J, Cheng Y, Pasic MD, Yousef GM. Liquid biopsy: a step forward towards precision medicine in urologic malignancies. Mol Cancer 2017; 16:80. [PMID: 28410618 PMCID: PMC5391592 DOI: 10.1186/s12943-017-0644-5] [Citation(s) in RCA: 246] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 03/28/2017] [Indexed: 12/12/2022] Open
Abstract
There is a growing trend towards exploring the use of a minimally invasive "liquid biopsy" to identify biomarkers in a number of cancers, including urologic malignancies. Multiple aspects can be assessed in circulating cell-free DNA, including cell-free DNA levels, integrity, methylation and mutations. Other prospective liquid biopsy markers include circulating tumor cells, circulating RNAs (miRNA, lncRNAs and mRNAs), cell-free proteins, peptides and exosomes have also emerged as non-invasive cancer biomarkers. These circulating molecules can be detected in various biological fluids, including blood, urine, saliva and seminal plasma. Liquid biopsies hold great promise for personalized medicine due to their ability to provide multiple non-invasive global snapshots of the primary and metastatic tumors. Molecular profiling of circulating molecules has been a stepping-stone to the successful introduction of several non-invasive multi-marker tests into the clinic. In this review, we provide an overview of the current state of cell-free DNA-based kidney, prostate and bladder cancer biomarker research and discuss the potential utility other circulating molecules. We will also discuss the challenges and limitations facing non-invasive cancer biomarker discovery and the benefits of this growing area of translational research.
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Affiliation(s)
- Ashley Di Meo
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
| | - Jenni Bartlett
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
| | - Yufeng Cheng
- Department of Radiation Oncology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Maria D Pasic
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Laboratory Medicine, St. Joseph's Health Centre, Toronto, ON, Canada
| | - George M Yousef
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada. .,Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada.
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22
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Khella HWZ, Daniel N, Youssef L, Scorilas A, Nofech-Mozes R, Mirham L, Krylov SN, Liandeau E, Krizova A, Finelli A, Cheng Y, Yousef GM. miR-10b is a prognostic marker in clear cell renal cell carcinoma. J Clin Pathol 2017; 70:854-859. [PMID: 28360191 DOI: 10.1136/jclinpath-2017-204341] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/09/2017] [Accepted: 03/10/2017] [Indexed: 12/21/2022]
Abstract
AIMS Clear cell renal cell carcinoma (ccRCC) is the most common adult kidney cancer. It is an aggressive tumour with unpredictable outcome. The currently used clinical parameters are not always accurate for predicting disease behaviour. miR-10b is dysregulated in different malignancies including RCC. METHODS We assessed the clinical utility of miR-10b as a prognostic marker in 250 patients with primary ccRCC. We examined the correlation between miR-10b and clinicopathological parameters. We compared miR-10b expression among different RCC subtypes and normal kidney tissue. RESULTS We observed a stepwise decrease of miR-10b expression from normal kidney to primary ccRCC and a further decrease from primary to metastatic RCC. miR-10b expression was significantly lower in stages III/IV compared with stages I/II (p=0.038). Using a binary cut-off, miR-10b-positive patients had significantly longer disease-free survival (HR=0.47, CI 0.28 to 0.79, p=0.004). In the subgroup of patients with tumour size >4 cm, higher miR-10b expression was associated with significant longer disease-free and overall survival (p=0.001 and p=0.036, respectively). miR-10b was significantly downregulated in ccRCC compared with normal kidney (p<0.0001), and oncocytoma (p=0.031). It was also downregulated in chromophobe RCC. In addition, we identified a number of miR-10b-predicted targets and pathways that are involved in tumourigenesis. CONCLUSIONS Our data point to miR-10b as a promising prognostic marker in ccRCC with potential therapeutic applications.
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Affiliation(s)
- Heba W Z Khella
- Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science at the Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Nicole Daniel
- Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science at the Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, Canada
| | - Leza Youssef
- Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science at the Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, Canada
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, University of Athens, Athens, Greece
| | - Roy Nofech-Mozes
- Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science at the Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, Canada
| | - Lorna Mirham
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Sergey N Krylov
- Department of Chemistry, Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, Canada
| | - Evi Liandeau
- Department of Chemistry, University of Athens, Athens, Greece
| | - Adriana Krizova
- Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science at the Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Antonio Finelli
- Division of Urologic Oncology, Department of Surgery, Princess Margaret Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Yufeng Cheng
- Department of Radiation Oncology, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - George M Yousef
- Department of Laboratory Medicine, Keenan Research Centre for Biomedical Science at the Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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23
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Velez DO, Mack H, Jupe J, Hawker S, Kulkarni N, Hedayatnia B, Zhang Y, Lawrence S, Fraley SI. Massively parallel digital high resolution melt for rapid and absolutely quantitative sequence profiling. Sci Rep 2017; 7:42326. [PMID: 28176860 PMCID: PMC5296755 DOI: 10.1038/srep42326] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 01/10/2017] [Indexed: 01/04/2023] Open
Abstract
In clinical diagnostics and pathogen detection, profiling of complex samples for low-level genotypes represents a significant challenge. Advances in speed, sensitivity, and extent of multiplexing of molecular pathogen detection assays are needed to improve patient care. We report the development of an integrated platform enabling the identification of bacterial pathogen DNA sequences in complex samples in less than four hours. The system incorporates a microfluidic chip and instrumentation to accomplish universal PCR amplification, High Resolution Melting (HRM), and machine learning within 20,000 picoliter scale reactions, simultaneously. Clinically relevant concentrations of bacterial DNA molecules are separated by digitization across 20,000 reactions and amplified with universal primers targeting the bacterial 16S gene. Amplification is followed by HRM sequence fingerprinting in all reactions, simultaneously. The resulting bacteria-specific melt curves are identified by Support Vector Machine learning, and individual pathogen loads are quantified. The platform reduces reaction volumes by 99.995% and achieves a greater than 200-fold increase in dynamic range of detection compared to traditional PCR HRM approaches. Type I and II error rates are reduced by 99% and 100% respectively, compared to intercalating dye-based digital PCR (dPCR) methods. This technology could impact a number of quantitative profiling applications, especially infectious disease diagnostics.
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Affiliation(s)
- Daniel Ortiz Velez
- Bioengineering Department, University of California San Diego, 92093, USA
| | - Hannah Mack
- Bioengineering Department, University of California San Diego, 92093, USA
| | - Julietta Jupe
- Bioengineering Department, University of California San Diego, 92093, USA
| | - Sinead Hawker
- Bioengineering Department, University of California San Diego, 92093, USA
| | - Ninad Kulkarni
- Electrical and Computer Engineering, University of California San Diego, 92093, USA
| | - Behnam Hedayatnia
- Electrical and Computer Engineering, University of California San Diego, 92093, USA
| | - Yang Zhang
- Bioengineering Department, University of California San Diego, 92093, USA
| | - Shelley Lawrence
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, University of California San Diego and Rady Children's Hospital of San Diego, 92093, USA
| | - Stephanie I Fraley
- Bioengineering Department, University of California San Diego, 92093, USA
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24
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Sidiropoulos KG, Ding Q, Pampalakis G, White NMA, Boulos P, Sotiropoulou G, Yousef GM. KLK6-regulated miRNA networks activate oncogenic pathways in breast cancer subtypes. Mol Oncol 2016; 10:993-1007. [PMID: 27093921 DOI: 10.1016/j.molonc.2016.03.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 03/28/2016] [Accepted: 03/31/2016] [Indexed: 12/21/2022] Open
Abstract
KLK6 is expressed in normal mammary tissues and is aberrantly regulated in breast cancer. At physiological levels of expression, i.e. those found in normal mammary tissues, KLK6 acts as a tumor suppressor in human breast cancer. However, aberrant overexpression of KLK6 (i.e. 50-100-fold higher than normal), a characteristic of a subset of human breast cancers is associated with increased tumorigenicity (Pampalakis et al. Cancer Res 69:3779-3787, 2009). Here, we stably transfected KLK6-non-expressing MDA-MB-231 breast cancer cells with the full-length KLK6 cDNA to overexpress KLK6 at levels comparable to those observed in patients, and investigated potential oncogenic miRNA networks regulated by these abnormally high KLK6 expression levels and increased activity of this serine protease. A number of miRNAs that are upregulated (e.g. miR-146a) or downregulated (e.g. miR-34a) via KLK6-induced alterations in the miRNA biogenesis machinery were identified. Integrated experimental and bioinformatics analyses identified convergent miRNA networks targeting the cell cycle, MYC, MAPK, and other signaling pathways. In large clinical datasets, significant correlations between KLK6 and downstream MAPK and MYC targets at both the RNA and protein levels was confirmed, as well as negative correlation with GATA3. It was also demonstrated that KLK6 overexpression and likely its proteolytic activity is associated with alterations in downstream miRNAs and their targets, and these differ with the molecular subtypes of breast cancer. The data partly explains the different characteristics of breast cancer subtypes. Importantly, we introduce a combined KLK6-CDKN1B+MYC+CDKN1C score for prediction of long-term patient survival outcomes, with higher scores indicating poor survival.
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Affiliation(s)
- Konstantinos G Sidiropoulos
- The Keenan Research Center in the Li Ka Shing Knowledge Institute and Department of Laboratory Medicine, St. Michael's Hospital, Toronto, M5B 1W8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, M5S 1A8, Canada
| | - Qiang Ding
- The Keenan Research Center in the Li Ka Shing Knowledge Institute and Department of Laboratory Medicine, St. Michael's Hospital, Toronto, M5B 1W8, Canada
| | | | - Nicole M A White
- The Keenan Research Center in the Li Ka Shing Knowledge Institute and Department of Laboratory Medicine, St. Michael's Hospital, Toronto, M5B 1W8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, M5S 1A8, Canada
| | - Peter Boulos
- The Keenan Research Center in the Li Ka Shing Knowledge Institute and Department of Laboratory Medicine, St. Michael's Hospital, Toronto, M5B 1W8, Canada
| | | | - George M Yousef
- The Keenan Research Center in the Li Ka Shing Knowledge Institute and Department of Laboratory Medicine, St. Michael's Hospital, Toronto, M5B 1W8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, M5S 1A8, Canada.
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25
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Hofmann E, Seeboeck R, Jacobi N, Obrist P, Huter S, Klein C, Oender K, Wiesner C, Hundsberger H, Eger A. The combinatorial approach of laser-captured microdissection and reverse transcription quantitative polymerase chain reaction accurately determines HER2 status in breast cancer. Biomark Res 2016; 4:8. [PMID: 27057311 PMCID: PMC4823853 DOI: 10.1186/s40364-016-0062-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/01/2016] [Indexed: 01/03/2023] Open
Abstract
Background HER2 expression in breast cancer correlates with increased metastatic potential, higher tumor recurrence rates and improved response to targeted therapies. Fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) are two methods commonly used for the analysis of HER2 in the clinic. However, lack of standardization, technical variability in laboratory protocols and subjective interpretation are major problems associated with these testing procedures. Methods Here we evaluated the applicability of reverse-transcription quantitative polymerase chain reaction (RT-qPCR) for HER2 testing in breast cancer. We tested thirty formaldehyde-fixed and paraffin-embedded tumor samples by RT-qPCR, FISH and IHC and analysed and compared the data from the three methods. Results We found that laser-captured microdissection is essential for the accurate determination of HER2 expression by RT-qPCR. When isolating RNA from total tumor tissue we obtained a significant number of false negative results. However, when using RNA from purified cancer cells the RT-qPCR data were fully consistent with FISH and IHC. In addition we provide evidence that ductal carcinomas might be further classified by the differential expression of HER3 and HER4. Conclusions Laser-captured microdissection in combination with RT-qPCR is a precise and cost-effective diagnostic approach for HER2 testing in cancer. The PCR assay is simple, accurate and robust and can easily be implemented and standardized in clinical laboratories.
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Affiliation(s)
- Elisabeth Hofmann
- Department Life Sciences, IMC University of Applied Sciences Krems, Piaristengasse 1, A-3500 Krems, Austria
| | - Rita Seeboeck
- Department Life Sciences, IMC University of Applied Sciences Krems, Piaristengasse 1, A-3500 Krems, Austria.,Pathology Laboratory Obrist and Brunhuber, Klostergasse 1, A-6511 Zams, Austria
| | - Nico Jacobi
- Department Life Sciences, IMC University of Applied Sciences Krems, Piaristengasse 1, A-3500 Krems, Austria
| | - Peter Obrist
- Pathology Laboratory Obrist and Brunhuber, Klostergasse 1, A-6511 Zams, Austria
| | - Samuel Huter
- Pathology Laboratory Obrist and Brunhuber, Klostergasse 1, A-6511 Zams, Austria
| | - Christian Klein
- Department Life Sciences, IMC University of Applied Sciences Krems, Piaristengasse 1, A-3500 Krems, Austria
| | - Kamil Oender
- Research Program for Rational Drug Design in Dermatology and Rheumatology, Department of Dermatology, Paracelsus Medical University of Salzburg, Müllner Hauptstraße 48, A-5020 Salzburg, Austria
| | - Christoph Wiesner
- Department Life Sciences, IMC University of Applied Sciences Krems, Piaristengasse 1, A-3500 Krems, Austria
| | - Harald Hundsberger
- Department Life Sciences, IMC University of Applied Sciences Krems, Piaristengasse 1, A-3500 Krems, Austria
| | - Andreas Eger
- Department Life Sciences, IMC University of Applied Sciences Krems, Piaristengasse 1, A-3500 Krems, Austria
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26
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Ibrahim R, Pasic M, Yousef GM. Omics for personalized medicine: defining the current we swim in. Expert Rev Mol Diagn 2016; 16:719-22. [PMID: 26959799 DOI: 10.1586/14737159.2016.1164601] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Rania Ibrahim
- a Department of Laboratory Medicine, and the Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute , St. Michael's Hospital , Toronto , Canada.,b Department of Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Canada
| | - Maria Pasic
- a Department of Laboratory Medicine, and the Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute , St. Michael's Hospital , Toronto , Canada.,b Department of Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Canada
| | - George M Yousef
- a Department of Laboratory Medicine, and the Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute , St. Michael's Hospital , Toronto , Canada.,b Department of Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Canada
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27
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miRNA-target network reveals miR-124as a key miRNA contributing to clear cell renal cell carcinoma aggressive behaviour by targeting CAV1 and FLOT1. Oncotarget 2016; 6:12543-57. [PMID: 26002553 PMCID: PMC4494957 DOI: 10.18632/oncotarget.3815] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 03/11/2015] [Indexed: 11/25/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is an aggressive tumor with frequent metastatic rate and poor survival. Integrated analyses allow understanding the interplay between different levels of molecular alterations. We integrated miRNA and gene expression data from 458 ccRCC and 254 normal kidney specimens to construct a miRNA-target interaction network. We identified the downregulated miR-124-3p, -30a-5p and -200c-3p as the most influential miRNAs in RCC pathogenesis.miR-124-3p and miR-200c-3p expression showed association with patient survival, miR-30a-5p was downregulated in metastases compared to primary tumors. We used an independent set of 87 matched samples for validation. We confirmed the functional impact of these miRNAs by in vitro assays. Restoration of these miRNAs reduced migration, invasion and proliferation. miR-124-3p decreased the S phase of cell cycle, as well. We compared transcriptome profiling before and after miRNA overexpression, and validated CAV1 and FLOT1 as miR-124-3p targets. Patients with higher CAV1 and FLOT1 had lower miR-124-3p expression and shorter overall survival. We hypothesize that these three miRNAs are fundamental contributing to ccRCC aggressive/metastatic behavior; and miR-124-3p especially has a key role through regulating CAV1 and FLOT1 expression. Restoration of the levels of these miRNAs could be considered as a potential therapeutic strategy for ccRCC.
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28
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Nofech-Mozes R, Khella HWZ, Scorilas A, Youssef L, Krylov SN, Lianidou E, Sidiropoulos KG, Gabril M, Evans A, Yousef GM. MicroRNA-194 is a Marker for Good Prognosis in Clear Cell Renal Cell Carcinoma. Cancer Med 2016; 5:656-64. [PMID: 26860079 PMCID: PMC4831284 DOI: 10.1002/cam4.631] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 11/25/2015] [Accepted: 12/07/2015] [Indexed: 12/25/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most prevalent adult kidney cancer. Prognostic markers are needed to guide patient management toward aggressive versus more conservative approaches, especially for small tumors ≤4 cm. miR‐194 was reported to be downregulated in several cancers and is involved in epithelial to mesenchymal transition. We evaluated miR‐194 as a prognostic marker in ccRCC. In a cohort of 234 patients with primary ccRCC, we correlated miR‐194 expression level with multiple clinicopathological features including disease‐free and overall survival, tumor size, clinical stage, and histological grade. Our results shows a stepwise decrease in miR‐194 expression from normal kidney to primary ccRCC (P = 0.0032) and a subsequent decrease from primary to metastatic lesions. Additionally, patients with higher miR‐194 expression has significantly longer disease‐free survival (P = 0.041) and overall survival (P = 0.031) compared to those with lower expression. In multivariate analysis, miR‐194‐positive tumors retain significance in disease‐free survival and overall survival, suggesting miR‐194 is an independent marker for good prognosis in ccRCC. Moreover, miR‐194 is a marker for good prognosis for patients with small renal masses (P = 0.014). These findings were validated on an independent data set from The Cancer Genome Atlas. We also compared miR‐194 expression between RCC subtypes. ccRCC had the highest levels, whereas chromophobe RCC and oncocytoma had comparable lower levels. Target prediction coupled with pathway analysis show that miR‐194 is predicted to target key molecules and pathways involved in RCC progression. miR‐194 represents a prognostic biomarker in ccRCC.
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Affiliation(s)
- Roy Nofech-Mozes
- Department of Laboratory Medicine and the Keenan Research Centre for Biomedical Science at the Li KaShing Knowledge Institute, St. Michael's Hospital, Toronto, M5B 1W8, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Heba W Z Khella
- Department of Laboratory Medicine and the Keenan Research Centre for Biomedical Science at the Li KaShing Knowledge Institute, St. Michael's Hospital, Toronto, M5B 1W8, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Andreas Scorilas
- Departments of Biochemistry and Molecular Biology, University of Athens, 15701, Athens, Greece
| | - Leza Youssef
- Department of Laboratory Medicine and the Keenan Research Centre for Biomedical Science at the Li KaShing Knowledge Institute, St. Michael's Hospital, Toronto, M5B 1W8, Canada
| | - Sergey N Krylov
- Departments of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Evi Lianidou
- Department of Chemistry, University of Athens, 15771, Athens, Greece
| | - Konstantinos G Sidiropoulos
- Department of Laboratory Medicine and the Keenan Research Centre for Biomedical Science at the Li KaShing Knowledge Institute, St. Michael's Hospital, Toronto, M5B 1W8, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Manal Gabril
- Department of Pathology, London Health Sciences Center and Western University, London, N6A 5W9, Canada
| | - Andrew Evans
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - George M Yousef
- Department of Laboratory Medicine and the Keenan Research Centre for Biomedical Science at the Li KaShing Knowledge Institute, St. Michael's Hospital, Toronto, M5B 1W8, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
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Abstract
Sepsis is a complex syndrome triggered by infection and characterized by systemic deregulation of immune and inflammatory pathways. It is a major cause of death worldwide and results in the widespread use of antibiotics and substantial health care costs. In a vicious circle, sepsis treatment promotes the emergence of highly virulent and resistant pathogens and devastating nosocomial infections. Sepsis is a heterogeneous disease affecting many people worldwide. Because individual patients have different inflammatory responses and unique profiles of immune activation against pathogens, the most effective way to advance the treatment of sepsis is probably through a tailored approach. The advent of high-throughput technologies and the remarkable progress in the field of bioinformatics has allowed the subclassification of many pathological conditions. This has potential to provide better understanding of life-threatening infections in people. The study of host factors, however, needs to be integrated with studies on bacterial signaling in both symbiotic and pathogenic bacteria. Sepsis is certainly the sum of multiple host-microbial interactions and the metagenome should be extensively investigated. Personalized medicine is probably the only strategy able to deconstruct and reassemble our knowledge about sepsis, and its use should allow us to understand and manipulate sepsis as a wide, interconnected phenomenon with myriad variables and peculiarities. In this study, the recent advances in this area, the major challenges that remain, and the reasons why the septic patient should be approached as a superorganism are discussed.
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30
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Burke E, Love R, Jones P, Fife T. Pharmacogenetic Testing: Application in Mental Health Prescribing. J Am Psychiatr Nurses Assoc 2016; 22:185-191. [PMID: 27009929 DOI: 10.1177/1078390316641488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Despite extensive scholastic and professional training, medication management in psychiatry is often relegated to trial-and-error prescribing. Pharmacogenetic testing (PGT) may expedite identification of medications with maximal efficacy and minimal side effects by recognizing individual genetic variability in drug response. OBJECTIVES This article outlines the background of PGT, explains drug metabolism, and evaluates the impact of PGT. DESIGN A review of the literature since 2010 found 42 articles regarding PGT in clinical nursing settings on PubMed and ProQuest. RESULTS Despite continuing rises in health care costs, new biotechnology has led to a decrease in the cost of genetic sequencing and application of PGT to practice. CONCLUSION As PGT becomes increasingly prevalent, nurses should be knowledgeable of its purpose, possibilities, and potential limitations to provide accurate and up-to-date patient information.
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Affiliation(s)
- Elizabeth Burke
- 1 Elizabeth Burke, DNP, PMHNP, Vanderbilt University School of Nursing, Nashville, TN, USA
| | - Rene Love
- 2 Rene Love, PhD, DNP, PMHNP-BC, FNAP, FAANP, University of Arizona School of Nursing, Tucson, AZ, USA
| | - Pam Jones
- 3 Pam Jones, DNP, NEA-BC, Vanderbilt School of Nursing, Nashville, TN, USA
| | - Taylor Fife
- 4 Taylor Fife, DNP, PMHNP-BC, Vanderbilt University School of Nursing, Nashville, TN, USA
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31
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Yousef GM. Personalized Medicine in Kidney Cancer: Learning How to Walk Before We Run. Eur Urol 2015; 68:1021-2. [DOI: 10.1016/j.eururo.2015.06.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 06/18/2015] [Indexed: 11/16/2022]
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32
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Belone ADFF, Rosa PS, Trombone APF, Fachin LRV, Guidella CC, Ura S, Barreto JA, Pinilla MG, de Carvalho AF, Carraro DM, Soares FA, Soares CT. Genome-Wide Screening of mRNA Expression in Leprosy Patients. Front Genet 2015; 6:334. [PMID: 26635870 PMCID: PMC4653304 DOI: 10.3389/fgene.2015.00334] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 11/05/2015] [Indexed: 11/13/2022] Open
Abstract
Leprosy, an infectious disease caused by Mycobacterium leprae, affects millions of people worldwide. However, little is known regarding its molecular pathophysiological mechanisms. In this study, a comprehensive assessment of human mRNA was performed on leprosy skin lesions by using DNA chip microarrays, which included the entire spectrum of the disease along with its reactional states. Sixty-six samples from leprotic lesions (10TT, 10BT, 10BB, 10BL, 4LL, 14R1, and 10R2) and nine skin biopsies from healthy individuals were used as controls (CC) (ages ranged from 06 to 83 years, 48 were male and 29 female). The evaluation identified 1580 differentially expressed mRNAs [Fold Change (FC) ≥ 2.0, p ≤ 0.05] in diseased lesions vs. healthy controls. Some of these genes were observed in all forms of the disease (CD2, CD27, chit1, FA2H, FAM26F, GZMB, MMP9, SLAMF7, UBD) and others were exclusive to reactional forms (Type "1" reaction: GPNMB, IL1B, MICAL2, FOXQ1; Type "2" reaction: AKR1B10, FAM180B, FOXQ1, NNMT, NR1D1, PTX3, TNFRSF25). In literature, these mRNAs have been associated with numerous pathophysiological processes and signaling pathways and are present in a large number of diseases. The role of these mRNAs maybe studied in the context of developing new diagnostic markers and therapeutic targets for leprosy.
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Affiliation(s)
- Andrea de Faria F Belone
- Department of Anatomic Pathology, Instituto Lauro de Souza Lima São Paulo, Brazil ; Department of Anatomic Pathology, A.C. Camargo Cancer Center São Paulo, Brazil
| | - Patrícia S Rosa
- Division of Research and Education, Instituto Lauro de Souza Lima São Paulo, Brazil
| | - Ana P F Trombone
- Department of Health Science, Universidade do Sagrado Coração São Paulo, Brazil
| | - Luciana R V Fachin
- Department of Anatomic Pathology, Instituto Lauro de Souza Lima São Paulo, Brazil
| | - Cássio C Guidella
- Ambulatory of Leprosy, Jardim Guanabara Health Center Rondonópolis, Brazil
| | - Somei Ura
- Division of Research and Education, Instituto Lauro de Souza Lima São Paulo, Brazil
| | - Jaison A Barreto
- Division of Dermathology, Instituto Lauro de Souza Lima São Paulo, Brazil
| | - Mabel G Pinilla
- Laboratory of Genomics and Molecular Biology, CIPE, A.C. Camargo Cancer Center Sao Paulo, Brazil
| | - Alex F de Carvalho
- Laboratory of Genomics and Molecular Biology, CIPE, A.C. Camargo Cancer Center Sao Paulo, Brazil
| | - Dirce M Carraro
- Laboratory of Genomics and Molecular Biology, CIPE, A.C. Camargo Cancer Center Sao Paulo, Brazil
| | - Fernando A Soares
- Department of Anatomic Pathology, A.C. Camargo Cancer Center São Paulo, Brazil
| | - Cleverson T Soares
- Department of Anatomic Pathology, Instituto Lauro de Souza Lima São Paulo, Brazil
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33
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S100A11 is a potential prognostic marker for clear cell renal cell carcinoma. Clin Exp Metastasis 2015; 33:63-71. [DOI: 10.1007/s10585-015-9758-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 10/08/2015] [Indexed: 12/13/2022]
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34
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White-Al Habeeb NM, Di Meo A, Scorilas A, Rotondo F, Masui O, Seivwright A, Gabril M, Girgis AHA, Jewett MA, Yousef GM. Alpha-enolase is a potential prognostic marker in clear cell renal cell carcinoma. Clin Exp Metastasis 2015; 32:531-41. [DOI: 10.1007/s10585-015-9725-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 05/27/2015] [Indexed: 01/20/2023]
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35
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Wala SJ, Karamchandani JR, Saleeb R, Evans A, Ding Q, Ibrahim R, Jewett M, Pasic M, Finelli A, Pace K, Lianidou E, Yousef GM. An integrated genomic analysis of papillary renal cell carcinoma type 1 uncovers the role of focal adhesion and extracellular matrix pathways. Mol Oncol 2015; 9:1667-77. [PMID: 26051997 DOI: 10.1016/j.molonc.2015.04.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 04/18/2015] [Accepted: 04/20/2015] [Indexed: 02/03/2023] Open
Abstract
Papillary renal cell carcinoma (pRCC) is the second most common RCC subtype and can be further classified as type 1 (pRCC1) or 2 (pRCC2). There is currently minimal understanding of pRCC1 pathogenesis, and treatment decisions are mostly empirical. The aim of this study was to identify biological pathways that are involved in pRCC1 pathogenesis using an integrated genomic approach. By microarray analysis, we identified a number of significantly dysregulated genes and microRNAs (miRNAs) that were unique to pRCC1. Integrated bioinformatics analyses showed enrichment of the focal adhesion and extracellular matrix (ECM) pathways. We experimentally validated that many members of these pathways are dysregulated in pRCC1. We identified and experimentally validated the downregulation of miR-199a-3p in pRCC1. Using cell line models, we showed that miR-199a-3p plays an important role in pRCC1 pathogenesis. Gain of function experiments showed that miR-199a-3p overexpression significantly decreased cell proliferation (p = 0.013). We also provide evidence that miR-199a-3p regulates the expression of genes linked to the focal adhesion and ECM pathways, such as caveolin 2 (CAV2), integrin beta 8 (ITGB8), MET proto-oncogene and mammalian target of rapamycin (MTOR). Using a luciferase reporter assay, we further provide evidence that miR-199a-3p overexpression decreases the expression of MET and MTOR. Using an integrated gene/miRNA approach, we provide evidence linking miRNAs to the focal adhesion and ECM pathways in pRCC1 pathogenesis. This novel information can contribute to the development of effective targeted therapies for pRCC1, for which there is none currently available in the clinic.
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Affiliation(s)
- Samantha Jane Wala
- The Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, Ontario M5B 1W8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.
| | - Jason Raj Karamchandani
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.
| | - Rola Saleeb
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.
| | - Andrew Evans
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada; Department of Pathology, Toronto General Hospital, Toronto, Ontario, Canada.
| | - Qiang Ding
- The Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, Ontario M5B 1W8, Canada.
| | - Rania Ibrahim
- The Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, Ontario M5B 1W8, Canada.
| | - Michael Jewett
- Department of Surgery, Princess Margaret Hospital, 610 University Avenue, Toronto, Ontario M5G 2M9, Canada.
| | - Maria Pasic
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada; Department of Laboratory Medicine, St. Joseph's Health Centre, 30 Queensway, Ontario M6R 1B5, Canada.
| | - Antonio Finelli
- Department of Surgery, Princess Margaret Hospital, 610 University Avenue, Toronto, Ontario M5G 2M9, Canada.
| | - Kenneth Pace
- Department of Surgery, St. Michael's Hospital, 30 Bond Street, Toronto, Ontario M5B 1W8, Canada.
| | - Evi Lianidou
- Laboratory of Analytical Chemistry, Department of Chemistry, University of Athens, 15771 Athens, Greece.
| | - George Makram Yousef
- The Keenan Research Centre in the Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, Ontario M5B 1W8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.
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37
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miR-210 is a prognostic marker in clear cell renal cell carcinoma. J Mol Diagn 2014; 17:136-44. [PMID: 25555365 DOI: 10.1016/j.jmoldx.2014.10.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 10/18/2014] [Accepted: 10/24/2014] [Indexed: 12/23/2022] Open
Abstract
Accurate assessment of prognosis of clear cell renal cell carcinoma (ccRCC) is key in optimizing management plans to fit individual patient needs. miRNAs are short noncoding single-stranded RNAs that control the expression of target genes and may act as cancer biomarkers. We analyzed the expression of miR-210 in 276 cases of primary ccRCC and compared its expression in 40 pairs of adjacent normal and cancerous tissues. We assessed its expression in primary and metastatic tumors, in the common RCC subtypes, and the benign oncocytoma. The results were validated with an independent data set from The Cancer Genome Atlas. miR-210 was significantly overexpressed in ccRCC compared with normal kidney. miR-210(+) patients had a statistically higher chance of disease recurrence [hazard ratio (HR), 1.82; P = 0.018] and shorter overall survival (HR, 2.46; P = 0.014). In multivariate analysis, miR-210 lost its statistically significant association with shorter disease-free survival and overall survival after adjusting for tumor size and tumor, node, metastasis stage. Papillary RCC showed comparable miR-210 overexpression, whereas decreased up-regulation was seen in chromophobe RCC and oncocytoma. A number of predicted targets that might be involved in carcinogenesis and aggressive tumor behavior were identified. miR-210 is a potential therapeutic target and independent marker of poor prognosis of ccRCC.
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Karamchandani JR, Gabril MY, Ibrahim R, Scorilas A, Filter E, Finelli A, Lee JY, Ordon M, Pasic M, Romaschin AD, Yousef GM. Profilin-1 expression is associated with high grade and stage and decreased disease-free survival in renal cell carcinoma. Hum Pathol 2014; 46:673-80. [PMID: 25704627 DOI: 10.1016/j.humpath.2014.11.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 11/13/2014] [Accepted: 11/14/2014] [Indexed: 12/18/2022]
Abstract
Clear cell renal cell carcinoma (ccRCC) is associated with high mortality, although individual outcomes are highly variable. Identification of patients with increased risk of disease progression can guide customizing management plan according to disease severity. Profilin-1 (Pfn1) has been recently identified as overexpressed in metastatic ccRCC compared with primary tumors. We examined Pfn1 expression in a tissue microarray of 384 cases of histologically confirmed primary ccRCC with detailed clinical follow-up. Profilin-1 expression showed both cytoplasmic and nuclear staining patterns. The immunoexpression of Pfn1 was scored in a semiquantitative fashion. There was no significant difference in Pfn1 expression between normal kidney and kidney ccRCC. Our results show that strong cytoplasmic Pfn1 expression is associated with high-grade (P < .001) and high-stage (III-IV) (P = .018) disease. Univariate analysis of the data set showed that higher Pfn1 expression is associated with significantly shorter disease-free survival (hazard ratio 7.36, P = .047) and also lower overall survival. Kaplan-Meier analysis showed that high cytoplasmic expression of Pfn1 was also associated with a statistically significant lower disease-free survival (P = .018). It was also associated with lower overall survival, although this was not statistically significant. Profilin-1 lost its prognostic significance in the multivariate analysis when controlling for grade and stage. Profilin-1 expression was not associated with significant prognostic deference in the subgroup of patients with stage 1 disease. Our results suggest that the evaluation of Pfn1 by immunohistochemistry may help to identify patients with an increased risk of disease progression. We validated our results at the messenger RNA level on an independent patient cohort. Higher messenger RNA expression of Pfn1 is associated with significantly lower survival.
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Affiliation(s)
- Jason R Karamchandani
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada M5S 1A8; Department of Laboratory Medicine and the Keenan Research Centre for Biomedical Science at the Li KaShing Knowledge Institute of St. Michael's Hospital, Toronto, Ontario, Canada M5B 1T8
| | | | - Rania Ibrahim
- Department of Laboratory Medicine and the Keenan Research Centre for Biomedical Science at the Li KaShing Knowledge Institute of St. Michael's Hospital, Toronto, Ontario, Canada M5B 1T8
| | | | - Emily Filter
- London Health Sciences, London, Ontario, Canada N6A 5A5
| | - Antonio Finelli
- Division of Urologic Oncology, Princess Margaret Hospital, University Health Network, Department of Surgery, University of Toronto, Toronto, Ontario, Canada M5G 2M9
| | - Jason Y Lee
- Division of Urology, St. Michael's Hospital, Toronto, Ontario, Canada M5B 1W8
| | - Michael Ordon
- Division of Urology, St. Michael's Hospital, Toronto, Ontario, Canada M5B 1W8
| | - Maria Pasic
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada M5S 1A8; Department of Laboratory Medicine, St. Joseph's Health Centre, Toronto, Ontario, Canada M6R 1B5
| | - Alexander D Romaschin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada M5S 1A8; Department of Laboratory Medicine and the Keenan Research Centre for Biomedical Science at the Li KaShing Knowledge Institute of St. Michael's Hospital, Toronto, Ontario, Canada M5B 1T8
| | - George M Yousef
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada M5S 1A8; Department of Laboratory Medicine and the Keenan Research Centre for Biomedical Science at the Li KaShing Knowledge Institute of St. Michael's Hospital, Toronto, Ontario, Canada M5B 1T8.
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Sidiropoulos KG, White NMA, Bui A, Ding Q, Boulos P, Pampalakis G, Khella H, Samuel JN, Sotiropoulou G, Yousef GM. Kallikrein-related peptidase 5 induces miRNA-mediated anti-oncogenic pathways in breast cancer. Oncoscience 2014; 1:709-24. [PMID: 25593998 PMCID: PMC4278268 DOI: 10.18632/oncoscience.91] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 10/23/2014] [Indexed: 12/15/2022] Open
Abstract
Kallikrein-related peptidase 5 (KLK5) displays aberrant expression in cancer. Recently, we showed KLK5 reconstitution in breast cancer cell lines suppresses malignancy. Present study aims to investigate the functional KLK5 mediated miRNA network on breast cancer progression, molecular subtype and survival. 28 miRNAs were up-regulated and 62 miRNAs were down-regulated upon KLK5 expression. Extracellular matrix (ECM) molecules and cell-adhesion pathways were the most significant KLK5-induced miRNA-mediated regulatory targets. Validation from The Cancer Genome Atlas (TCGA) database indicated KLK5 was specifically down-regulated in luminal B and basal-like breast cancer subtypes. There was a correlation between KLK5, miRNAs and their downstream ECM gene targets. Long-term patient survival correlated with dysregulation of KLK5 and interacting ECM target genes. It suggests biological differences between breast cancer molecular subtypes, patient survival, and their propensity for invasion and metastasis can be explained in part by altered miRNA networks induced by KLK5 dysregulation. We provide the first evidence that KLK5 can affect miRNA networks, which regulate MMPs and other novel ECM targets and a new compelling hypothesis of interplay between serine proteases and miRNAs. We developed a combined KLK5-(ITGB1+COL12A1) predictive score for recurrence-free survival that could be exploited in clinical applications.
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Affiliation(s)
- Konstantinos G Sidiropoulos
- The Keenan Research Center for Biomedical Sciences at the Li Ka Shing Knowledge Institute and Department of Laboratory Medicine, St. Michael's Hospital, Toronto, Canada ; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Nicole M A White
- The Keenan Research Center for Biomedical Sciences at the Li Ka Shing Knowledge Institute and Department of Laboratory Medicine, St. Michael's Hospital, Toronto, Canada ; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Anna Bui
- The Keenan Research Center for Biomedical Sciences at the Li Ka Shing Knowledge Institute and Department of Laboratory Medicine, St. Michael's Hospital, Toronto, Canada
| | - Qiang Ding
- The Keenan Research Center for Biomedical Sciences at the Li Ka Shing Knowledge Institute and Department of Laboratory Medicine, St. Michael's Hospital, Toronto, Canada
| | - Peter Boulos
- The Keenan Research Center for Biomedical Sciences at the Li Ka Shing Knowledge Institute and Department of Laboratory Medicine, St. Michael's Hospital, Toronto, Canada
| | - Georgios Pampalakis
- Department of Pharmacy, School of Health Sciences, University of Patras, Rion-Patras, Greece
| | - Heba Khella
- The Keenan Research Center for Biomedical Sciences at the Li Ka Shing Knowledge Institute and Department of Laboratory Medicine, St. Michael's Hospital, Toronto, Canada
| | - Joseph N Samuel
- The Keenan Research Center for Biomedical Sciences at the Li Ka Shing Knowledge Institute and Department of Laboratory Medicine, St. Michael's Hospital, Toronto, Canada
| | - Georgia Sotiropoulou
- Department of Pharmacy, School of Health Sciences, University of Patras, Rion-Patras, Greece
| | - George M Yousef
- The Keenan Research Center for Biomedical Sciences at the Li Ka Shing Knowledge Institute and Department of Laboratory Medicine, St. Michael's Hospital, Toronto, Canada ; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
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40
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Chang CQ, Tingle SR, Filipski KK, Khoury MJ, Lam TK, Schully SD, Ioannidis JPA. An overview of recommendations and translational milestones for genomic tests in cancer. Genet Med 2014; 17:431-40. [PMID: 25341115 DOI: 10.1038/gim.2014.133] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/20/2014] [Indexed: 11/09/2022] Open
Abstract
PURPOSE To understand the translational trajectory of genomic tests in cancer screening, diagnosis, prognosis, and treatment, we reviewed tests that have been assessed by recommendation and guideline developers. METHODS For each test, we marked translational milestones by determining when the genomic association with cancer was first discovered and studied in patients, and when a health application for a specified clinical use was successfully demonstrated and approved or cleared by the US Food and Drug Administration. To identify recommendations and guidelines, we reviewed the websites of cancer, genomic, and general guideline developers and professional organizations. We searched the in vitro diagnostics database of the US Food and Drug Administration for information, and we searched PubMed for translational milestones. Milestones were examined against type of recommendation, Food and Drug Administration approval or clearance, disease rarity, and test purpose. RESULTS Of the 45 tests we identified, 9 received strong recommendations for their usage in clinical settings, 14 received positive but moderate recommendations, and 22 were not currently recommended. For 18 tests, two or more different sources had issued recommendations, with 67% concordance. Only five tests had Food and Drug Administration approval, and an additional five had clearance. The median time from discovery to recommendation statement was 14.7 years. CONCLUSION In general, there were no associations found between translational trajectory and recommendation category.Genet Med 17 6, 431-440.
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Affiliation(s)
- Christine Q Chang
- Epidemiology and Genomics Research Program, National Cancer Institute, Rockville, Maryland, USA
| | - Sharna R Tingle
- Epidemiology and Genomics Research Program, National Cancer Institute, Rockville, Maryland, USA
| | - Kelly K Filipski
- Epidemiology and Genomics Research Program, National Cancer Institute, Rockville, Maryland, USA
| | - Muin J Khoury
- 1] Epidemiology and Genomics Research Program, National Cancer Institute, Rockville, Maryland, USA [2] Office of Public Health Genomics, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Tram Kim Lam
- Epidemiology and Genomics Research Program, National Cancer Institute, Rockville, Maryland, USA
| | - Sheri D Schully
- Epidemiology and Genomics Research Program, National Cancer Institute, Rockville, Maryland, USA
| | - John P A Ioannidis
- 1] Epidemiology and Genomics Research Program, National Cancer Institute, Rockville, Maryland, USA [2] Stanford Prevention Research Center, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA [3] Department of Health Research and Policy, Stanford University School of Medicine, Stanford, California, USA [4] Department of Statistics, Stanford University School of Humanities and Sciences, Stanford, California, USA
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DeGracia DJ, Tri Anggraini F, Taha DTM, Huang ZF. Inductive and Deductive Approaches to Acute Cell Injury. INTERNATIONAL SCHOLARLY RESEARCH NOTICES 2014; 2014:859341. [PMID: 27437490 PMCID: PMC4897055 DOI: 10.1155/2014/859341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 06/25/2014] [Indexed: 11/28/2022]
Abstract
Many clinically relevant forms of acute injury, such as stroke, traumatic brain injury, and myocardial infarction, have resisted treatments to prevent cell death following injury. The clinical failures can be linked to the currently used inductive models based on biological specifics of the injury system. Here we contrast the application of inductive and deductive models of acute cell injury. Using brain ischemia as a case study, we discuss limitations in inductive inferences, including the inability to unambiguously assign cell death causality and the lack of a systematic quantitative framework. These limitations follow from an overemphasis on qualitative molecular pathways specific to the injured system. Our recently developed nonlinear dynamical theory of cell injury provides a generic, systematic approach to cell injury in which attractor states and system parameters are used to quantitatively characterize acute injury systems. The theoretical, empirical, and therapeutic implications of shifting to a deductive framework are discussed. We illustrate how a deductive mathematical framework offers tangible advantages over qualitative inductive models for the development of therapeutics of acutely injured biological systems.
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Affiliation(s)
- Donald J. DeGracia
- Department of Physiology, Wayne State University, 4116 Scott Hall, 540 East Canfield Avenue, Detroit, MI 48201, USA
| | - Fika Tri Anggraini
- Department of Physiology, Wayne State University, 4116 Scott Hall, 540 East Canfield Avenue, Detroit, MI 48201, USA
| | | | - Zhi-Feng Huang
- Department of Physics and Astronomy, Wayne State University, Detroit, MI 48201, USA
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Girgis H, Masui O, White NM, Scorilas A, Rotondo F, Seivwright A, Gabril M, Filter ER, Girgis AH, Bjarnason GA, Jewett MA, Evans A, Al-Haddad S, Siu KM, Yousef GM. Lactate dehydrogenase A is a potential prognostic marker in clear cell renal cell carcinoma. Mol Cancer 2014; 13:101. [PMID: 24885701 PMCID: PMC4022787 DOI: 10.1186/1476-4598-13-101] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 04/22/2014] [Indexed: 12/17/2022] Open
Abstract
Background Over 90% of cancer-related deaths in clear cell renal cell carcinoma (RCC) are caused by tumor relapse and metastasis. Thus, there is an urgent need for new molecular markers that can potentiate the efficacy of the current clinical-based models of prognosis assessment. The objective of this study is to evaluate the potential significance of lactate dehydrogenase A (LDHA), assessed by immunohistochemical staining, as a prognostic marker in clear cell renal cell carcinoma in relation to clinicopathological features and clinical outcome. Methods We assessed the expression of LDHA at the protein level, by immunohistochemistry, and correlated its expression with multiple clinicopathological features including tumor size, clinical stage, histological grade, disease-free and overall survival in 385 patients with primary clear cell renal cell carcinoma. We also correlated the LDHA expression with overall survival, at mRNA level, in an independent data set of 170 clear cell renal cell carcinoma cases from The Cancer Genome Atlas databases. Cox proportional hazards models adjusted for the potential clinicopathological factors were used to test for associations between the LDHA expression and both disease-free survival and overall survival. Results There is statistically significant positive correlation between LDHA level of expression and tumor size, clinical stage and histological grade. Moreover, LDHA expression shows significantly inverse correlation with both disease-free survival and overall survival in patients with clear cell renal cell carcinoma. Our results are validated by examining LDHA expression, at the mRNA level, in the independent data set of clear cell renal cell carcinoma cases from The Cancer Genome Atlas databases which also shows that higher lactate dehydrogenase A expression is associated with significantly shorter overall survival. Conclusion Our results indicate that LDHA up-regulation can be a predictor of poor prognosis in clear cell renal cell carcinoma. Thus, it represents a potential prognostic biomarker that can boost the accuracy of other prognostic models in patients with clear cell renal cell carcinoma.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - George M Yousef
- The Keenan Research Center in the Li Ka Shing Knowledge Institute, St, Michael's Hospital, Toronto M5B 1 W8, Canada.
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Li A, Meyre D. Jumping on the Train of Personalized Medicine: A Primer for Non- Geneticist Clinicians: Part 3. Clinical Applications in the Personalized Medicine Area. CURRENT PSYCHIATRY REVIEWS 2014; 10:118-132. [PMID: 25598768 PMCID: PMC4287884 DOI: 10.2174/1573400510666140630170549] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 05/27/2014] [Accepted: 05/29/2014] [Indexed: 12/17/2022]
Abstract
The rapid decline of sequencing costs brings hope that personal genome sequencing will become a common feature of medical practice. This series of three reviews aim to help non-geneticist clinicians to jump into the fast-moving field of personalized genetic medicine. In the first two articles, we covered the fundamental concepts of molecular genetics and the methodologies used in genetic epidemiology. In this third article, we discuss the evolution of personalized medicine and illustrate the most recent success in the fields of Mendelian and complex human diseases. We also address the challenges that currently limit the use of personalized medicine to its full potential.
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Affiliation(s)
| | - David Meyre
- Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, ON L8N 3Z5, Canada
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Hodgkin Disease Therapy Induced Second Malignancy Susceptibility 6q21 Functional Variants in Roma and Hungarian Population Samples. Pathol Oncol Res 2013; 20:529-33. [DOI: 10.1007/s12253-013-9724-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 11/11/2013] [Indexed: 10/25/2022]
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Fraley SI, Hardick J, Masek BJ, Jo Masek B, Athamanolap P, Rothman RE, Gaydos CA, Carroll KC, Wakefield T, Wang TH, Yang S. Universal digital high-resolution melt: a novel approach to broad-based profiling of heterogeneous biological samples. Nucleic Acids Res 2013; 41:e175. [PMID: 23935121 PMCID: PMC3794612 DOI: 10.1093/nar/gkt684] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Comprehensive profiling of nucleic acids in genetically heterogeneous samples is important for clinical and basic research applications. Universal digital high-resolution melt (U-dHRM) is a new approach to broad-based PCR diagnostics and profiling technologies that can overcome issues of poor sensitivity due to contaminating nucleic acids and poor specificity due to primer or probe hybridization inaccuracies for single nucleotide variations. The U-dHRM approach uses broad-based primers or ligated adapter sequences to universally amplify all nucleic acid molecules in a heterogeneous sample, which have been partitioned, as in digital PCR. Extensive assay optimization enables direct sequence identification by algorithm-based matching of melt curve shape and Tm to a database of known sequence-specific melt curves. We show that single-molecule detection and single nucleotide sensitivity is possible. The feasibility and utility of U-dHRM is demonstrated through detection of bacteria associated with polymicrobial blood infection and microRNAs (miRNAs) associated with host response to infection. U-dHRM using broad-based 16S rRNA gene primers demonstrates universal single cell detection of bacterial pathogens, even in the presence of larger amounts of contaminating bacteria; U-dHRM using universally adapted Lethal-7 miRNAs in a heterogeneous mixture showcases the single copy sensitivity and single nucleotide specificity of this approach.
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Affiliation(s)
- Stephanie I Fraley
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA, Department of Emergency Medicine, The Johns Hopkins University, Baltimore, MD 21218, USA, Division of Infectious Disease, Department of Medicine, The Johns Hopkins University, Baltimore, MD 21218, USA, Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University, Baltimore, MD 21218, USA, The Johns Hopkins Hospital, Baltimore, MD 21287, USA and Department of Mechanical Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA
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