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Rayamajhi S, Sipes J, Tetlow AL, Saha S, Bansal A, Godwin AK. Extracellular Vesicles as Liquid Biopsy Biomarkers across the Cancer Journey: From Early Detection to Recurrence. Clin Chem 2024; 70:206-219. [PMID: 38175602 DOI: 10.1093/clinchem/hvad176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 09/26/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Cancer is a dynamic process and thus requires highly informative and reliable biomarkers to help guide patient care. Liquid-based biopsies have emerged as a clinical tool for tracking cancer dynamics. Extracellular vesicles (EVs), lipid bilayer delimited particles secreted by cells, are a new class of liquid-based biomarkers. EVs are rich in selectively sorted biomolecule cargos, which provide a spatiotemporal fingerprint of the cell of origin, including cancer cells. CONTENT This review summarizes the performance characteristics of EV-based biomarkers at different stages of cancer progression, from early malignancy to recurrence, while emphasizing their potential as diagnostic, prognostic, and screening biomarkers. We discuss the characteristics of effective biomarkers, consider challenges associated with the EV biomarker field, and report guidelines based on the biomarker discovery pipeline. SUMMARY Basic science and clinical trial studies have shown the potential of EVs as precision-based biomarkers for tracking cancer status, with promising applications for diagnosing disease, predicting response to therapy, and tracking disease burden. The multi-analyte cargos of EVs enhance the performance characteristics of biomarkers. Recent technological advances in ultrasensitive detection of EVs have shown promise with high specificity and sensitivity to differentiate early-cancer cases vs healthy individuals, potentially outperforming current gold-standard imaging-based cancer diagnosis. Ultimately, clinical translation will be dictated by how these new EV biomarker-based platforms perform in larger sample cohorts. Applying ultrasensitive, scalable, and reproducible EV detection platforms with better design considerations based upon the biomarker discovery pipeline should guide the field towards clinically useful liquid biopsy biomarkers.
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Affiliation(s)
- Sagar Rayamajhi
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Jared Sipes
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Ashley L Tetlow
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Souvik Saha
- Division of Gastroenterology and Hepatology, University of Kansas Health System, Kansas City, KS, United States
| | - Ajay Bansal
- Division of Gastroenterology and Hepatology, University of Kansas Health System, Kansas City, KS, United States
- The University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, United States
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
- The University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, United States
- Division of Genomic Diagnostics, University of Kansas Health System, Kansas City, KS, United States
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, KS, United States
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2
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Lou J, Liu K, Wen J, He Y, Sun Y, Tian X, Hu K, Deng Y, Liu B, Wen G. Deciphering the neural mechanisms of miR-134 in major depressive disorder with population-based and person-specific imaging transcriptomic techniques. Psychiatry Res 2023; 329:115551. [PMID: 37871377 DOI: 10.1016/j.psychres.2023.115551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/07/2023] [Accepted: 10/17/2023] [Indexed: 10/25/2023]
Abstract
MiR-134 has emerged as a potential molecular biomarker for the detection and management of major depressive disorder (MDD). Nevertheless, the specific effects of miR-134 as a regulatory element on brain function and its implications for the clinical presentation of MDD are not yet fully understood. In order to investigate the potential neural mechanisms that contribute to the relationship between miR-134 and MDD, we employed a parallel two-stage cross-scale multi-omics approach. This involved utilizing the anterior cingulate cortex (ACC) functional connectivity as a means to connect microscopic molecular structures with macroscopic brain function in two separate cohorts: the MDD-I dataset (56 MDD patients and 51 healthy controls) and the MDD-II dataset (57 MDD patients and 52 healthy controls). We found a stable ACC functional dysconnectivity pattern of MDD and established the hierarchical cross-scale association from molecular organizations of miR-134 target genes to macroscopic brain functional dysconnectivity and associated behavior, as revealed by population-based analysis. Additionally, our person-specific imaging transcriptomic study revealed that individual exosomal miR-134 expression levels impact on individual clinical symptoms of MDD by modulating ACC-related functional dysconnectivity. Together, our findings provide compelling evidence of the correlation between miR-134 and depression across multi scales within the gene-brain-behavior context.
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Affiliation(s)
- Jing Lou
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, China
| | - Kai Liu
- School of Medical Imaging, Xuzhou Medical University, Xuzhou 221006,China; Department of Radiology, Affiliated Hospital of Xuzhou Medical University, Xuzhou Medical University, Xuzhou 221004,China
| | - Junyan Wen
- Department of Imaging, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yini He
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, China
| | - Yuqing Sun
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, China
| | - Xiaohan Tian
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, China
| | - Ke Hu
- Brainnetome Center and National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China; School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing 100049,China
| | - Yanjia Deng
- School of Medical Imaging, Xuzhou Medical University, Xuzhou 221006,China.
| | - Bing Liu
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, China; IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing 100875, China; Chinese Institute for Brain Research, Beijing 102206, China.
| | - Ge Wen
- Department of Imaging, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.
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3
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Iijima H, Wang K, D'Amico E, Tang WY, Rogers RJ, Jakicic JM, Ambrosio F. Exercise-primed extracellular vesicles improve cell-matrix adhesion and chondrocyte health. RESEARCH SQUARE 2023:rs.3.rs-2958821. [PMID: 37333349 PMCID: PMC10274961 DOI: 10.21203/rs.3.rs-2958821/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Extracellular vesicles (EVs) have been suggested to transmit the health-promoting effects of exercise throughout the body. Yet, the mechanisms by which beneficial information is transmitted from extracellular vesicles to recipient cells are poorly understood, precluding a holistic understanding of how exercise promotes cellular and tissue health. In this study, using articular cartilage as a model, we introduced a network medicine paradigm to simulate how exercise facilitates communication between circulating EVs and chondrocytes, the cells resident in articular cartilage. Using the archived small RNA-seq data of EV before and after aerobic exercise, microRNA regulatory network analysis based on network propagation inferred that circulating EVs activated by aerobic exercise perturb chondrocyte-matrix interactions and downstream cellular aging processes. Building on the mechanistic framework identified through computational analyses, follow up experimental studies interrogated the direct influence of exercise on EV-mediated chondrocyte-matrix interactions. We found that pathogenic matrix signaling in chondrocytes was abrogated in the presence of exercise-primed EVs, restoring a more youthful phenotype, as determined by chondrocyte morphological profiling and evaluation of chondrogenicity. Epigenetic reprograming of the gene encoding the longevity protein, α-Klotho, mediated these effects. These studies provide mechanistic evidence that exercise transduces rejuvenation signals to circulating EVs, endowing EVs with the capacity to ameliorate cellular health even in the presence of an unfavorable microenvironmental signals.
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Affiliation(s)
- Hirotaka Iijima
- Institute for Advanced Research, Nagoya University, Nagoya, Japan
- Biomedical and Health Informatics Unit, Graduate School of Medicine, Nagoya University, Nagoya, Japan
- Department of Physical Medicine and Rehabilitation, University of Pittsburgh, Pittsburgh, PA
| | - Kai Wang
- Discovery Center for Musculoskeletal Recovery, Schoen Adams Research Institute at Spaulding, Boston, MA
- Department of Physical Medicine & Rehabilitation, Harvard Medical School, Boston, MA
| | - Ella D'Amico
- Department of Physical Medicine and Rehabilitation, University of Pittsburgh, Pittsburgh, PA
| | - Wan-Yee Tang
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA
| | - Renee J Rogers
- Department of Internal Medicine, Division of Physical Activity and Weight Management, University of Kansas Medical Center, Kansas City, KS
| | - John M Jakicic
- Department of Internal Medicine, Division of Physical Activity and Weight Management, University of Kansas Medical Center, Kansas City, KS
| | - Fabrisia Ambrosio
- Department of Physical Medicine and Rehabilitation, University of Pittsburgh, Pittsburgh, PA
- Discovery Center for Musculoskeletal Recovery, Schoen Adams Research Institute at Spaulding, Boston, MA
- Department of Physical Medicine & Rehabilitation, Harvard Medical School, Boston, MA
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4
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Hanin A, Cespedes J, Pulluru Y, Gopaul M, Aronica E, Decampo D, Helbig I, Howe CL, Huttner A, Koh S, Navarro V, Taraschenko O, Vezzani A, Wilson MR, Xian J, Gaspard N, Hirsch LJ. Review and standard operating procedures for collection of biospecimens and analysis of biomarkers in new onset refractory status epilepticus. Epilepsia 2023; 64:1444-1457. [PMID: 37039049 PMCID: PMC10756682 DOI: 10.1111/epi.17600] [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: 01/06/2023] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/12/2023]
Abstract
New onset refractory status epilepticus (NORSE), including its subtype with a preceding febrile illness known as febrile infection-related epilepsy syndrome (FIRES), is one of the most severe forms of status epilepticus. The exact causes of NORSE are currently unknown, and there is so far no disease-specific therapy. Identifying the underlying pathophysiology and discovering specific biomarkers, whether immunologic, infectious, genetic, or other, may help physicians in the management of patients with NORSE. A broad spectrum of biomarkers has been proposed for status epilepticus patients, some of which were evaluated for patients with NORSE. Nonetheless, none has been validated, due to significant variabilities in study cohorts, collected biospecimens, applied analytical methods, and defined outcome endpoints, and to small sample sizes. The NORSE Institute established an open NORSE/FIRES biorepository for health-related data and biological samples allowing the collection of biospecimens worldwide, promoting multicenter research and sharing of data and specimens. Here, we suggest standard operating procedures for biospecimen collection and biobanking in this rare condition. We also propose criteria for the appropriate use of previously collected biospecimens. We predict that the widespread use of standardized procedures will reduce heterogeneity, facilitate the future identification of validated biomarkers for NORSE, and provide a better understanding of the pathophysiology and best clinical management for these patients.
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Affiliation(s)
- Aurélie Hanin
- Department of Neurology and Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
- Sorbonne Université, Institut du Cerveau ICM, Paris Brain Institute, Inserm, CNRS, Assistance Publique -Hôpitaux de Paris, Hôpital de la Pitié-Salpêtrière, DMU Neurosciences 6, Paris, France
- Assistance Publique -Hôpitaux de Paris, Hôpital de la Pitié-Salpêtrière, DMU Neurosciences 6, Epilepsy Unit and Department of Clinical Neurophysiology, Paris, France
| | - Jorge Cespedes
- Comprehensive Epilepsy Center, Department of Neurology, Yale University School of Medicine, New Haven, Connecticut, USA
- Universidad Autonoma de Centro America, School of Medicine, San Jose, Costa Rica
| | - Yashwanth Pulluru
- Comprehensive Epilepsy Center, Department of Neurology, Yale University School of Medicine, New Haven, Connecticut, USA
- Nebraska Medical Center, Omaha, Nebraska, USA
| | - Margaret Gopaul
- Comprehensive Epilepsy Center, Department of Neurology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Eleonora Aronica
- Department of (Neuro) Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Danielle Decampo
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Epilepsy NeuroGenetics Initiative, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ingo Helbig
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Epilepsy NeuroGenetics Initiative, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Charles L. Howe
- Division of Experimental Neurology, Mayo Clinic, Rochester, Minnesota, USA
- Center for Multiple Sclerosis and Autoimmune Neurology, Mayo Clinic, Rochester, Minnesota, USA
| | - Anita Huttner
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sookyong Koh
- Department of Pediatrics, Children’s Hospital Medical Center, University of Nebraska, Omaha, Nebraska, USA
| | - Vincent Navarro
- Sorbonne Université, Institut du Cerveau ICM, Paris Brain Institute, Inserm, CNRS, Assistance Publique -Hôpitaux de Paris, Hôpital de la Pitié-Salpêtrière, DMU Neurosciences 6, Paris, France
- Assistance Publique -Hôpitaux de Paris, Hôpital de la Pitié-Salpêtrière, DMU Neurosciences 6, Epilepsy Unit and Department of Clinical Neurophysiology, Paris, France
| | - Olga Taraschenko
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Annamaria Vezzani
- Department of Acute Brain Injury, Istituto di Recerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Michael R. Wilson
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, California, San Francisco, USA
| | - Julie Xian
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Epilepsy NeuroGenetics Initiative, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Nicolas Gaspard
- Comprehensive Epilepsy Center, Department of Neurology, Yale University School of Medicine, New Haven, Connecticut, USA
- Université Libre de Bruxelles, Hôpital Erasme, Brussels, Belgium
| | - Lawrence J. Hirsch
- Comprehensive Epilepsy Center, Department of Neurology, Yale University School of Medicine, New Haven, Connecticut, USA
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5
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REMARK guidelines for tumour biomarker study reporting: a remarkable history. Br J Cancer 2023; 128:443-445. [PMID: 36476656 PMCID: PMC9938190 DOI: 10.1038/s41416-022-02046-4] [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: 09/27/2022] [Revised: 10/17/2022] [Accepted: 10/21/2022] [Indexed: 12/12/2022] Open
Abstract
In 2005, several experts in tumor biomarker research publishe the REporting recommendations for Tumor MARKer prognostic studies (REMARK) criteria. Coupled with the subsequent Biospecimen Reporting for Improved Study Quality (BRISQ) criteria, these initiatives provide a framework for transparently reporting of the methods of study conduct and analyses.
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6
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Kalinin RS, Goleva OV, Illarionov RA, Tsai VV, Mukomolova AL, Konstantinova YE, Markin IV, Krylov AV, Rogozina NV, Bekhtereva MK, Tyan MS, Orlova ED, Donnikov MY, Kovalenko LV, Kolbasin LN, Glotov AS, Glotov OS. Development of a biobank in the structure of scientific and diagnostic and treatment institutions and prospects for interregional integration. КАРДИОВАСКУЛЯРНАЯ ТЕРАПИЯ И ПРОФИЛАКТИКА 2022. [DOI: 10.15829/1728-8800-2022-3401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The formation of biobanks in the structure of scientific and treatment and diagnostic institutions with prospects for interregional integration is a fundamental link in monitoring and predicting diseases of various origins, creating and testing highly effective diagnostics, and developing novel therapeutic agents.Aim. To describe standard operating procedures and principles for the formation of bioresource collections (BRC) in medical institutions with biobanking.Material and methods. The data of scientific and practical biomedical projects using BRC obtained from patients with genetic, multifactorial and infectious diseases in St. Petersburg and Surgut are presented. As of September 2022, the BRC collected on the basis of the Pediatric Research and Clinical Center for Infectious Diseases of the Federal Medical and Biological Agency includes biosamples from 1619 patients, and the BRC collected in the Medical Institute of Surgut State University includes biosamples from 450 patients and healthy individuals of different sex and age. The selection of biosamples from apparently healthy individuals and patients with various diseases can serve as a strategically important resource for future research in terms of etiology, epidemiology, the development of regulatory environment and scales, innovations in the development of diagnostic approaches and treatment of the Russian population.
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Affiliation(s)
- R. S. Kalinin
- Pediatric Research and Clinical Center for Infectious Diseases of the Federal Medical and Biological Agency;
D.O. Ott Research Institute of Obstetrics, Gynecology, and Reproductology;
Surgut State University
| | - O. V. Goleva
- Pediatric Research and Clinical Center for Infectious Diseases of the Federal Medical and Biological Agency
| | - R. A. Illarionov
- D.O. Ott Research Institute of Obstetrics, Gynecology, and Reproductology;
Surgut State University
| | - V. V. Tsai
- Pediatric Research and Clinical Center for Infectious Diseases of the Federal Medical and Biological Agency;
D.O. Ott Research Institute of Obstetrics, Gynecology, and Reproductology
| | - A. L. Mukomolova
- Pediatric Research and Clinical Center for Infectious Diseases of the Federal Medical and Biological Agency
| | - Yu. E. Konstantinova
- Pediatric Research and Clinical Center for Infectious Diseases of the Federal Medical and Biological Agency
| | - I. V. Markin
- Pediatric Research and Clinical Center for Infectious Diseases of the Federal Medical and Biological Agency
| | - A. V. Krylov
- Pediatric Research and Clinical Center for Infectious Diseases of the Federal Medical and Biological Agency
| | - N. V. Rogozina
- Pediatric Research and Clinical Center for Infectious Diseases of the Federal Medical and Biological Agency
| | - M. K. Bekhtereva
- Pediatric Research and Clinical Center for Infectious Diseases of the Federal Medical and Biological Agency
| | - M. S. Tyan
- Pediatric Research and Clinical Center for Infectious Diseases of the Federal Medical and Biological Agency
| | - E. D. Orlova
- Pediatric Research and Clinical Center for Infectious Diseases of the Federal Medical and Biological Agency
| | | | | | | | - A. S. Glotov
- D.O. Ott Research Institute of Obstetrics, Gynecology, and Reproductology
| | - O. S. Glotov
- Pediatric Research and Clinical Center for Infectious Diseases of the Federal Medical and Biological Agency;
D.O. Ott Research Institute of Obstetrics, Gynecology, and Reproductology
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7
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López-Guerrero JA, Mendiola M, Pérez-Fidalgo JA, Romero I, Torres A, Recalde D, Molina E, Gómez-Raposo C, Levin AM, Herrero A, Alarcón J, Esteban C, Marquina G, Rubio MJ, Guerra E, Sánchez-Lorenzo L, Gálvez-Montosa F, de Juan A, Churruca C, Gallego A, González-Martín A. Prospective Real-World Gynaecological Cancer Clinical Registry with Associated Biospecimens: A Collaborative Model to Promote Translational Research between GEICO and the Spanish Biobank Network. Cancers (Basel) 2022; 14:cancers14081965. [PMID: 35454870 PMCID: PMC9031046 DOI: 10.3390/cancers14081965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 02/04/2023] Open
Abstract
Patient registries linked to biorepositories constitute a valuable asset for clinical and translational research in oncology. The Spanish Group of Ovarian Cancer Research (GEICO), in collaboration with the Spanish Biobank Network (RNBB), has developed a multicentre, multistakeholder, prospective virtual clinical registry (VCR) associated with biobanks for the collection of real-world data and biological samples of gynaecological cancer patients. This collaborative project aims to promote research by providing broad access to high-quality clinical data and biospecimens for future research according to the needs of investigators and to increase diagnostic and therapeutic opportunities for gynaecological cancer patients in Spain. The VCR will include the participation of more than 60 Spanish hospitals entering relevant clinical information in harmonised electronic case report forms (eCRFs) in four different cohorts: ovarian, endometrial, cervical, and rare gynaecological cancers (gestational trophoblastic disease). Initial data for the cases included till December 2021 are presented. The model described herein establishes a real-world win-win collaboration between multicentre structures, promoted and supported by GEICO, that will contribute to the success of translational research in gynaecological cancer.
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Affiliation(s)
- José Antonio López-Guerrero
- Laboratorio de Biología Molecular y Biobanco, Fundación Instituto Valenciano de Oncología, 46009 Valencia, Spain
- Unidad Mixta de Investigación en Cáncer IVO-CIPF, Centro de Investigación Príncipe Felipe (CIPF), 46012 Valencia, Spain
- Departamento de Patología, Facultad de Medicina, Universidad Católica de Valencia ‘San Vicente Martir’, 46001 Valencia, Spain
- Correspondence: ; Tel.: +34-961114337
| | - Marta Mendiola
- Laboratorio de Patología Molecular y Dianas Terapéuticas, Instituto de Investigación Hospital Universitario La Paz (IdiPAZ), 28029 Madrid, Spain;
- Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - José Alejandro Pérez-Fidalgo
- Departamento de Oncología Médica, Hospital Clinico de Valencia, Instituto de Investigación Sanitaria INCLIVA, Universidad de Valencia, CIBERONC, 46010 Valencia, Spain;
| | - Ignacio Romero
- Department of Medical Oncology, Fundación Instituto Valenciano de Oncología, 46009 Valencia, Spain;
| | - Ana Torres
- Biobanco del Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain;
| | - Delia Recalde
- Biobanco del Sistema de Salud de Aragón, 50009 Zaragoza, Spain;
| | - Elena Molina
- Biobanco del Hospital Clínico San Carlos, 28040 Madrid, Spain;
| | - César Gómez-Raposo
- Department of Medical Oncology, Hospital Universitario Infanta Sofía, 28703 Madrid, Spain;
| | - Ana M. Levin
- Grupo Español de Investigación en Cáncer de Ovario, 28003 Madrid, Spain;
| | - Ana Herrero
- Department of Medical Oncology, Hospital Universitario Miguel Servet, 50009 Zaragoza, Spain;
| | - Jesús Alarcón
- Department of Medical Oncology, Hospital Universitario Son Espases, 07120 Palma, Spain;
| | - Carmen Esteban
- Department of Medical Oncology, Hospital Virgen de la Salud, 45004 Toledo, Spain;
| | - Gloria Marquina
- Department of Medical Oncology, Hospital Clínico San Carlos, 28040 Madrid, Spain;
| | - María Jesús Rubio
- Department of Medical Oncology, Hospital Universitario Reina Sofía, 14004 Córdoba, Spain;
| | - Eva Guerra
- Department of Medical Oncology, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain;
| | - Luisa Sánchez-Lorenzo
- Department of Medical Oncology, Clínica Universidad de Navarra, 28027 Madrid, Spain; (L.S.-L.); (A.G.-M.)
| | | | - Ana de Juan
- Department of Medical Oncology, Hospital Univeristario Marqués de Valdecilla, 39008 Santander, Spain;
| | - Cristina Churruca
- Department of Medical Oncology, Hospital Universitario Donostia, 20014 Donostia, Spain;
| | - Alejandro Gallego
- Department of Medical Oncology, Hospital Universitario La Paz, 28029 Madrid, Spain;
| | - Antonio González-Martín
- Department of Medical Oncology, Clínica Universidad de Navarra, 28027 Madrid, Spain; (L.S.-L.); (A.G.-M.)
- Programa de Tumores Sólidos, Centro de Investigación de Medicina Aplicada (CIMA), 31008 Pamplona, Spain
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8
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Wotton L, Gali B, Carvalho K, Tarling T, Matzke L, Watson PH. Analysis of Trends in Biospecimen Complexity in Cancer Research Over Two Decades. Biopreserv Biobank 2021; 20:195-200. [PMID: 34515517 DOI: 10.1089/bio.2021.0078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Background: Over time, researchers' demand for increased quality and quantity of biospecimens has risen. However, quality is multifaceted, ranging from simple to complex, and comes at a cost. Therefore, to be sustainable and ensure optimal utilization of their resources (supply), biobanks must consider the trends in biospecimen use to predict the needs for future biospecimen quality (demand). Methods: An unbiased selection process was used to identify research articles from across the spectrum of cancer research from the PubMed database. A set of 225 articles utilizing human biospecimens were randomly selected for review (75 articles from each of three time intervals; 2000, 2010, 2020). Criteria for determining the source and complexity of quality of biospecimens were developed and overall concordance between two independent observers abstracting the data was then confirmed (k = 0.87) to validate the criteria. Results: We observed increased use of dual biospecimen formats (20%-36% of articles, p = 0.03), matched samples (16%-37% of articles, p = 0.0033), and biospecimens with associated outcomes data (20%-49%, p = 0.0002). In addition, the use of two or more cohorts increased over time (p = 0.03). The mechanism through which biospecimens were obtained also changed over time with an increase in the diversity of collection pathways used (p = 0.006). Conclusions: The complexity of biospecimens being used in cancer research and the diversity of collection pathways through which these are obtained has changed significantly. This observation is important for biobanks given that the cost to support the supply of biospecimens with complex extrinsic as opposed to simple intrinsic quality characteristics is greater. For biobanks to manage sustainability, optimize utilization, and meet changing research demand, they may need to adjust their operational models to better support the supply of these types of biospecimens.
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Affiliation(s)
- Lauren Wotton
- Island Medical Program, University of British Columbia, Victoria, Canada
| | - Brent Gali
- Biobanking and Biospecimen Research Services, Deeley Research Centre, BC Cancer, Victoria, Canada
| | - Karlene Carvalho
- Biobanking and Biospecimen Research Services, Deeley Research Centre, BC Cancer, Victoria, Canada
| | - Tamsin Tarling
- Biobanking and Biospecimen Research Services, Deeley Research Centre, BC Cancer, Victoria, Canada
| | - Lise Matzke
- Biobanking and Biospecimen Research Services, Deeley Research Centre, BC Cancer, Victoria, Canada
| | - Peter H Watson
- Biobanking and Biospecimen Research Services, Deeley Research Centre, BC Cancer, Victoria, Canada.,Canadian Tissue Repository Network, Vancouver, Canada
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9
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Claassen J, Akbari Y, Alexander S, Bader MK, Bell K, Bleck TP, Boly M, Brown J, Chou SHY, Diringer MN, Edlow BL, Foreman B, Giacino JT, Gosseries O, Green T, Greer DM, Hanley DF, Hartings JA, Helbok R, Hemphill JC, Hinson HE, Hirsch K, Human T, James ML, Ko N, Kondziella D, Livesay S, Madden LK, Mainali S, Mayer SA, McCredie V, McNett MM, Meyfroidt G, Monti MM, Muehlschlegel S, Murthy S, Nyquist P, Olson DM, Provencio JJ, Rosenthal E, Sampaio Silva G, Sarasso S, Schiff ND, Sharshar T, Shutter L, Stevens RD, Vespa P, Videtta W, Wagner A, Ziai W, Whyte J, Zink E, Suarez JI. Proceedings of the First Curing Coma Campaign NIH Symposium: Challenging the Future of Research for Coma and Disorders of Consciousness. Neurocrit Care 2021; 35:4-23. [PMID: 34236619 PMCID: PMC8264966 DOI: 10.1007/s12028-021-01260-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/15/2021] [Indexed: 01/04/2023]
Abstract
Coma and disorders of consciousness (DoC) are highly prevalent and constitute a burden for patients, families, and society worldwide. As part of the Curing Coma Campaign, the Neurocritical Care Society partnered with the National Institutes of Health to organize a symposium bringing together experts from all over the world to develop research targets for DoC. The conference was structured along six domains: (1) defining endotype/phenotypes, (2) biomarkers, (3) proof-of-concept clinical trials, (4) neuroprognostication, (5) long-term recovery, and (6) large datasets. This proceedings paper presents actionable research targets based on the presentations and discussions that occurred at the conference. We summarize the background, main research gaps, overall goals, the panel discussion of the approach, limitations and challenges, and deliverables that were identified.
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Affiliation(s)
- Jan Claassen
- Department of Neurology, Columbia University and New York-Presbyterian Hospital, 177 Fort Washington Avenue, MHB 8 Center, Room 300, New York City, NY, 10032, USA.
| | - Yama Akbari
- Departments of Neurology, Neurological Surgery, and Anatomy & Neurobiology and Beckman Laser Institute and Medical Clinic, University of California, Irvine, Irvine, CA, USA
| | - Sheila Alexander
- Acute and Tertiary Care, School of Nursing and Critical Care Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Kathleen Bell
- Department of Physical Medicine and Rehabilitation, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Thomas P Bleck
- Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Melanie Boly
- Department of Neurology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Jeremy Brown
- Office of Emergency Care Research, Division of Clinical Research, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Sherry H-Y Chou
- Departments of Critical Care Medicine, Neurology, and Neurosurgery, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael N Diringer
- Department of Neurology, Washington University in St. Louis, St. Louis, MO, USA
| | - Brian L Edlow
- Department of Neurology, Center for Neurotechnology and Neurorecovery, Massachusetts General Hospital and Harvard Medical School, Harvard University, Boston, MA, USA
| | - Brandon Foreman
- Departments of Neurology and Rehabilitation Medicine, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Joseph T Giacino
- Department of Physical Medicine and Rehabilitation, Harvard Medical School, Harvard University, Boston, MA, USA
| | - Olivia Gosseries
- GIGA Consciousness After Coma Science Group, University of Liege, Liege, Belgium
| | - Theresa Green
- School of Nursing, Queensland University of Technology, Kelvin Grove, QLD, Australia
| | - David M Greer
- Department of Neurology, School of Medicine, Boston University, Boston, MA, USA
| | - Daniel F Hanley
- Division of Brain Injury Outcomes, Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Jed A Hartings
- Department of Neurosurgery, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Raimund Helbok
- Neurocritical Care Unit, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - J Claude Hemphill
- Department of Neurology, Weill Institute for Neurosciences, School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - H E Hinson
- Department of Neurology, School of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Karen Hirsch
- Department of Neurology, Stanford University, Palo Alto, CA, USA
| | - Theresa Human
- Department of Pharmacy, Barnes Jewish Hospital, St. Louis, MO, USA
| | - Michael L James
- Departments of Anesthesiology and Neurology, Duke University, Durham, NC, USA
| | - Nerissa Ko
- Department of Neurology, Weill Institute for Neurosciences, School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel Kondziella
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Neurology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Sarah Livesay
- College of Nursing, Rush University, Chicago, IL, USA
| | - Lori K Madden
- Center for Nursing Science, University of California, Davis, Sacramento, CA, USA
| | - Shraddha Mainali
- Department of Neurology, The Ohio State University, Columbus, OH, USA
| | - Stephan A Mayer
- Department of Neurology, New York Medical College, Valhalla, NY, USA
| | - Victoria McCredie
- Interdepartmental Division of Critical Care, Department of Respirology, University of Toronto, Toronto, ON, Canada
| | - Molly M McNett
- College of Nursing, The Ohio State University, Columbus, OH, USA
| | - Geert Meyfroidt
- Department of Intensive Care Medicine, University Hospitals Leuven and University of Leuven, Leuven, Belgium
| | - Martin M Monti
- Departments of Neurosurgery and Psychology, Brain Injury Research Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Susanne Muehlschlegel
- Departments of Neurology, Anesthesiology/Critical Care, and Surgery, Medical School, University of Massachusetts, Worcester, MA, USA
| | - Santosh Murthy
- Department of Neurology, Weill Cornell Medical College, New York City, NY, USA
| | - Paul Nyquist
- Division of Neurosciences Critical Care, Departments of Anesthesiology and Critical Care Medicine, Neurology, and Neurosurgery, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - DaiWai M Olson
- Departments of Neurology and Neurosurgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - J Javier Provencio
- Departments of Neurology and Neuroscience, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Eric Rosenthal
- Department of Neurology, Harvard Medical School, Harvard University, Boston, MA, USA
| | - Gisele Sampaio Silva
- Department of Neurology, Albert Einstein Israelite Hospital and Universidade Federal de São Paulo, São Paulo, Brazil
| | - Simone Sarasso
- Department of Biomedical and Clinical Sciences "L. Sacco", Università degli Studi di Milano, Milan, Italy
| | - Nicholas D Schiff
- Department of Neurology and Brain Mind Research Institute, Weill Cornell Medicine, Cornell University, New York City, NY, USA
| | - Tarek Sharshar
- Department of Intensive Care, Paris Descartes University, Paris, France
| | - Lori Shutter
- Departments of Critical Care Medicine, Neurology, and Neurosurgery, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Robert D Stevens
- Division of Neurosciences Critical Care, Departments of Anesthesiology and Critical Care Medicine, Neurology, and Neurosurgery, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Paul Vespa
- Departments of Neurosurgery and Neurology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Walter Videtta
- National Hospital Alejandro Posadas, Buenos Aires, Argentina
| | - Amy Wagner
- Department of Physical Medicine and Rehabilitation, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wendy Ziai
- Division of Neurosciences Critical Care, Departments of Anesthesiology and Critical Care Medicine, Neurology, and Neurosurgery, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - John Whyte
- Moss Rehabilitation Research Institute, Elkins Park, PA, USA
| | - Elizabeth Zink
- Division of Neurosciences Critical Care, Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Jose I Suarez
- Division of Neurosciences Critical Care, Departments of Anesthesiology and Critical Care Medicine, Neurology, and Neurosurgery, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
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10
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Byrne JA, Carpenter JE, Carter C, Phillips K, Braye S, Watson PH, Rush A. Building Research Support Capacity across Human Health Biobanks during the COVID-19 Pandemic. Biomark Insights 2021; 16:11772719211024100. [PMID: 34177256 PMCID: PMC8207259 DOI: 10.1177/11772719211024100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/12/2021] [Indexed: 11/23/2022] Open
Abstract
Human health biobanks are forms of research infrastructure that supply biospecimens and associated data to researchers, and therefore juxtapose the activities of clinical care and biomedical research. The discipline of biobanking has existed for over 20 years and is supported by several international professional societies and dedicated academic journals. However, despite both rising research demand for human biospecimens, and the growth of biobanking as an academic discipline, many individual biobanks continue to experience sustainability challenges. This commentary will summarize how the COVID-19 pandemic is creating new challenges and opportunities for both the health biobanking sector and the supporting discipline of biobanking. While the challenges for biobanks may be numerous and acute, there are opportunities for both individual biobanks and the discipline of biobanking to embrace change such that biobanks can continue to support and drive biomedical research. We will therefore describe numerous practical steps that individual biobanks and/or the discipline of biobanking can take to survive and possibly thrive in response to the COVID-19 pandemic.
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Affiliation(s)
- Jennifer A Byrne
- New South Wales Health Statewide Biobank, New South Wales Health Pathology, Camperdown, NSW, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Jane E Carpenter
- New South Wales Health Pathology, Newcastle, NSW, Australia.,Scientific Platforms, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - Candace Carter
- New South Wales Health Statewide Biobank, New South Wales Health Pathology, Camperdown, NSW, Australia
| | - Kathleen Phillips
- New South Wales Health Statewide Biobank, New South Wales Health Pathology, Camperdown, NSW, Australia
| | - Stephen Braye
- New South Wales Health Pathology, Newcastle, NSW, Australia
| | - Peter H Watson
- Biobanking and Biospecimen Research Services, Deeley Research Centre, BC Cancer Agency, Victoria, BC, Canada.,Canadian Tissue Repository Network, Vancouver, BC, Canada
| | - Amanda Rush
- New South Wales Health Statewide Biobank, New South Wales Health Pathology, Camperdown, NSW, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, NSW, Australia
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11
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Ma L, Sahu SK, Cano M, Kuppuswamy V, Bajwa J, McPhatter J, Pine A, Meizlish ML, Goshua G, Chang CH, Zhang H, Price C, Bahel P, Rinder H, Lei T, Day A, Reynolds D, Wu X, Schriefer R, Rauseo AM, Goss CW, O’Halloran JA, Presti RM, Kim AH, Gelman AE, Dela Cruz CS, Lee AI, Mudd PA, Chun HJ, Atkinson JP, Kulkarni HS. Increased complement activation is a distinctive feature of severe SARS-CoV-2 infection. Sci Immunol 2021; 6:eabh2259. [PMID: 34446527 PMCID: PMC8158979 DOI: 10.1126/sciimmunol.abh2259] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/11/2021] [Indexed: 12/13/2022]
Abstract
Complement activation has been implicated in the pathogenesis of severe SARS-CoV-2 infection. However, it remains to be determined whether increased complement activation is a broad indicator of critical illness (and thus, no different in COVID-19). It is also unclear which pathways are contributing to complement activation in COVID-19, and if complement activation is associated with certain features of severe SARS-CoV-2 infection, such as endothelial injury and hypercoagulability. To address these questions, we investigated complement activation in the plasma from patients with COVID-19 prospectively enrolled at two tertiary care centers: Washington University School of Medicine (n=134) and Yale School of Medicine (n=49). We compared our patients to two non-COVID cohorts: (a) patients hospitalized with influenza (n=54), and (b) patients admitted to the intensive care unit (ICU) with acute respiratory failure requiring invasive mechanical ventilation (IMV, n=22). We demonstrate that circulating markers of complement activation are elevated in patients with COVID-19 compared to those with influenza and to patients with non-COVID-19 respiratory failure. Further, the results facilitate distinguishing those who are at higher risk of worse outcomes such as requiring ICU admission, or IMV. Moreover, the results indicate enhanced activation of the alternative complement pathway is most prevalent in patients with severe COVID-19 and is associated with markers of endothelial injury (i.e., angiopoietin-2) as well as hypercoagulability (i.e., thrombomodulin and von Willebrand factor). Our findings identify complement activation to be a distinctive feature of COVID-19, and provide specific targets that may be utilized for risk prognostication, drug discovery and personalized clinical trials.
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Affiliation(s)
- Lina Ma
- Division of Pulmonary and Critical Care Medicine, John T. Milliken Department of Medicine, Washington University School of Medicine; St. Louis, USA
| | - Sanjaya K. Sahu
- Division of Pulmonary and Critical Care Medicine, John T. Milliken Department of Medicine, Washington University School of Medicine; St. Louis, USA
| | - Marlene Cano
- Division of Pulmonary and Critical Care Medicine, John T. Milliken Department of Medicine, Washington University School of Medicine; St. Louis, USA
| | - Vasanthan Kuppuswamy
- Division of Hospital Medicine, John T. Milliken Department of Medicine, Washington University School of Medicine; St. Louis, USA
| | - Jamal Bajwa
- Division of Pulmonary and Critical Care Medicine, John T. Milliken Department of Medicine, Washington University School of Medicine; St. Louis, USA
- Marian University; Indianapolis, USA
| | - Ja’Nia McPhatter
- Division of Pulmonary and Critical Care Medicine, John T. Milliken Department of Medicine, Washington University School of Medicine; St. Louis, USA
- University of Pittsburgh; Pittsburgh, USA
| | - Alexander Pine
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine; New Haven, USA
| | | | - George Goshua
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine; New Haven, USA
| | - C-Hong Chang
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine; New Haven, USA
| | - Hanming Zhang
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine; New Haven, USA
| | - Christina Price
- Section of Immunology, Department of Internal Medicine, Yale School of Medicine; New Haven, USA
| | | | | | - Tingting Lei
- Department of Pathology and Immunology, Washington University School of Medicine; St. Louis, USA
| | - Aaron Day
- Department of Emergency Medicine, Washington University School of Medicine; St. Louis, USA
| | - Daniel Reynolds
- Division of Pulmonary and Critical Care Medicine, John T. Milliken Department of Medicine, Washington University School of Medicine; St. Louis, USA
| | - Xiaobo Wu
- Division of Rheumatology, John T. Milliken Department of Medicine, Washington University School of Medicine; St. Louis, USA
| | - Rebecca Schriefer
- Division of Rheumatology, John T. Milliken Department of Medicine, Washington University School of Medicine; St. Louis, USA
| | - Adriana M. Rauseo
- Division of Infectious Diseases, John T. Milliken Department of Medicine, Washington University School of Medicine; St. Louis, USA
| | - Charles W. Goss
- Division of Biostatistics, Washington University School of Medicine; St. Louis, USA
| | - Jane A. O’Halloran
- Division of Infectious Diseases, John T. Milliken Department of Medicine, Washington University School of Medicine; St. Louis, USA
| | - Rachel M. Presti
- Division of Infectious Diseases, John T. Milliken Department of Medicine, Washington University School of Medicine; St. Louis, USA
| | - Alfred H. Kim
- Division of Rheumatology, John T. Milliken Department of Medicine, Washington University School of Medicine; St. Louis, USA
| | - Andrew E. Gelman
- Department of Pathology and Immunology, Washington University School of Medicine; St. Louis, USA
- Division of Biostatistics, Washington University School of Medicine; St. Louis, USA
| | - Charles S. Dela Cruz
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine; New Haven, USA
| | - Alfred I. Lee
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine; New Haven, USA
| | - Philip A. Mudd
- Department of Emergency Medicine, Washington University School of Medicine; St. Louis, USA
| | - Hyung J. Chun
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine; New Haven, USA
| | - John P. Atkinson
- Division of Rheumatology, John T. Milliken Department of Medicine, Washington University School of Medicine; St. Louis, USA
| | - Hrishikesh S. Kulkarni
- Division of Pulmonary and Critical Care Medicine, John T. Milliken Department of Medicine, Washington University School of Medicine; St. Louis, USA
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12
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Lim SJ, Gurusamy K, O'Connor D, Shaaban AM, Brierley D, Lewis I, Harrison D, Kendall TJ, Robinson M. Recommendations for cellular and molecular pathology input into clinical trials: a systematic review and meta-aggregation. J Pathol Clin Res 2021; 7:191-202. [PMID: 33635586 PMCID: PMC8073003 DOI: 10.1002/cjp2.199] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/11/2020] [Accepted: 01/03/2021] [Indexed: 01/10/2023]
Abstract
The SPIRIT (Standard Protocol Items: Recommendations for Interventional Trials) 2013 Statement was developed to provide guidance for inclusion of key methodological components in clinical trial protocols. However, these standards do not include guidance specific to pathology input in clinical trials. This systematic review aims to synthesise existing recommendations specific to pathology practice in clinical trials for implementation in trial protocol design. Articles were identified from database searches and deemed eligible for inclusion if they contained: (1) guidance and/or a checklist, which was (2) pathology-related, with (3) content relevant to clinical trial protocols or could influence a clinical trial protocol design from a pathology perspective and (4) were published in 1996 or later. The quality of individual papers was assessed using the AGREE-GRS (Appraisal of Guidelines for REsearch & Evaluation - Global Rating Scale) tool, and the confidence in cumulative evidence was evaluated using the GRADE-CERQual (Grading of Recommendations Assessment, Development and Evaluation-Confidence in Evidence from Reviews of Qualitative research) approach. Extracted recommendations were synthesised using the best fit framework method, which includes thematic analysis followed by a meta-aggregative approach to synthesis within the framework. Of the 10 184 records screened and 199 full-text articles reviewed, only 40 guidance resources met the eligibility criteria for inclusion. Recommendations extracted from 22 guidance documents were generalisable enough for data synthesis. Seven recommendation statements were synthesised as follows: (1) multidisciplinary collaboration in trial design with early involvement of pathologists, particularly with respect to the use of biospecimens and associated biomarker/analytical assays and in the evaluation of pathology-related parameters; (2) funding and training for personnel undertaking trial work; (3) selection of an accredited laboratory with suitable facilities to undertake scheduled work; (4) quality assurance of pathology-related parameters; (5) transparent reporting of pathology-related parameters; (6) policies regarding informatics and tracking biospecimens across trial sites; and (7) informed consent for specimen collection and retention for future research.
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Affiliation(s)
- Shujing Jane Lim
- Department of Cellular PathologyNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle Upon TyneUK
- Division of Surgery and Interventional SciencesUniversity College LondonLondonUK
| | - Kurinchi Gurusamy
- Division of Surgery and Interventional SciencesUniversity College LondonLondonUK
| | - Daniel O'Connor
- The Medicines and Healthcare Products Regulatory AgencyLondonUK
| | - Abeer M Shaaban
- Department of HistopathologyQueen Elizabeth Hospital BirminghamBirminghamUK
- Institute of Cancer and Genomic SciencesUniversity of BirminghamBirminghamUK
| | - Daniel Brierley
- Unit of Oral and Maxillofacial PathologyUniversity of SheffieldSheffieldUK
| | - Ian Lewis
- National Cancer Research InstituteLondonUK
| | | | - Timothy James Kendall
- University of Edinburgh Centre for Inflammation Research, University of EdinburghEdinburghUK
| | - Max Robinson
- Department of Cellular PathologyNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle Upon TyneUK
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13
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Suganuma N, Kawachi K, Yamashita T, Yamanaka T, Sugawara Y, Matsubara Y, Yamazaki H, Kohagura K, Toda S, Okamoto S, Yoshida T, Rino Y, Masuda M, Narimatsu H, Fujita H, Yoshioka E, Yokose T, Furuta K, Miyagi Y. Quality Control of Breast Cancer Surgery Samples: Introducing Time Stamp Checking. Biopreserv Biobank 2021; 19:369-375. [PMID: 33926234 DOI: 10.1089/bio.2020.0133] [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: 11/13/2022] Open
Abstract
Background: Analytical information obtained from clinical tissue samples has recently become more important due to recent advancements in the clinical practice of medicine, for example, gene panel testing. However, acquiring and managing the sample quality, which greatly influences the analyses, are not sufficient and hence requires immediate attention. We introduced time stamp (TS) recording and documentation using the Standard PREanalytical Code (SPREC) for breast cancer surgery samples to monitor and control their quality. Materials and Methods: The TS recording used SPREC for quality control of each sample by recording seven factors: type of sample, type of collection, warm ischemia time (WIT), cold ischemia time (CIT), fixation type, fixation time (FT), and long-term storage. The responsibilities to record each factor were assigned among group members (breast surgeons, anesthesiologists, pathologists, operating room nurses, and medical technologists in pathology). Results: Records based on SPREC were recorded for 393 surgical cases of first-time breast cancer patients performed at the Kanagawa Cancer Center from May 2018 to April 2019. The vascular clamp time was defined as when skin flap formation was completed, regardless of the surgical procedure. An anesthesiologist recorded the vascular clamp time and sample collection time, and the pathologist recorded the fixation start time and fixation end time. WIT was 23 (3-116) minutes (breast-conserving surgery, 11 [3-38] minutes; mastectomy, 26 [5-116] minutes; and nipple-sparing mastectomy, 39 [31-43] minutes), CIT was 37 (3-1052) minutes, and FT was 43 (17-115) hours. The median CIT and FT were significantly shortened after introducing the TS system, and the variabilities were reduced. Conclusion: A TS system for quality control of breast cancer surgical sample functions well due to the establishment of highly versatile WIT and a working group consisting of multiple members of different occupations who shared roles.
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Affiliation(s)
- Nobuyasu Suganuma
- Department of Surgery, Yokohama City University, Yokohama, Japan.,Department of Breast and Endocrine Surgery, Kanagawa Cancer Center, Yokohama, Japan
| | - Kae Kawachi
- Department of Pathology, Kanagawa Cancer Center, Yokohama, Japan
| | - Toshinari Yamashita
- Department of Breast and Endocrine Surgery, Kanagawa Cancer Center, Yokohama, Japan
| | - Takashi Yamanaka
- Department of Breast and Endocrine Surgery, Kanagawa Cancer Center, Yokohama, Japan
| | - Yuko Sugawara
- Department of Breast and Endocrine Surgery, Kanagawa Cancer Center, Yokohama, Japan
| | - Yuka Matsubara
- Department of Breast and Endocrine Surgery, Kanagawa Cancer Center, Yokohama, Japan
| | - Haruhiko Yamazaki
- Department of Breast and Endocrine Surgery, Kanagawa Cancer Center, Yokohama, Japan
| | - Kaori Kohagura
- Department of Breast and Endocrine Surgery, Kanagawa Cancer Center, Yokohama, Japan
| | - Soji Toda
- Department of Breast and Endocrine Surgery, Kanagawa Cancer Center, Yokohama, Japan
| | - Saki Okamoto
- Department of Breast and Endocrine Surgery, Kanagawa Cancer Center, Yokohama, Japan
| | - Tatsuya Yoshida
- Department of Surgery, Yokohama City University, Yokohama, Japan
| | - Yasushi Rino
- Department of Surgery, Yokohama City University, Yokohama, Japan
| | - Munetaka Masuda
- Department of Surgery, Yokohama City University, Yokohama, Japan
| | - Hiroto Narimatsu
- Cancer Prevention and Control Division, Kanagawa Cancer Center Research Institute, Yokohama, Japan
| | - Hisae Fujita
- Department of Anesthesiology, Kanagawa Cancer Center, Yokohama, Japan
| | - Emi Yoshioka
- Department of Pathology, Kanagawa Cancer Center, Yokohama, Japan
| | - Tomonori Yokose
- Department of Pathology, Kanagawa Cancer Center, Yokohama, Japan
| | - Koh Furuta
- Division of Clinical Laboratory, Kanagawa Cancer Center, Yokohama, Japan
| | - Yohei Miyagi
- Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, Yokohama, Japan
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14
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Schinke H, Heider T, Herkommer T, Simon F, Blancke Soares A, Kranz G, Samaga D, Dajka L, Feuchtinger A, Walch A, Valeanu L, Walz C, Kirchner T, Canis M, Baumeister P, Belka C, Maihöfer C, Marschner S, Pflugradt U, Ganswindt U, Hess J, Zitzelsberger H, Gires O. Digital scoring of EpCAM and slug expression as prognostic markers in head and neck squamous cell carcinomas. Mol Oncol 2020; 15:1040-1053. [PMID: 33340247 PMCID: PMC8024715 DOI: 10.1002/1878-0261.12886] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/11/2020] [Accepted: 12/15/2020] [Indexed: 02/06/2023] Open
Abstract
Head and neck squamous cell carcinomas (HNSCCs) have poor clinical outcome owing to therapy resistance and frequent recurrences that are among others attributable to tumor cells in partial epithelial‐to‐mesenchymal transition (pEMT). We compared side‐by‐side software‐based and visual quantification of immunohistochemistry (IHC) staining of epithelial marker EpCAM and EMT regulator Slug in n = 102 primary HNSCC to assess optimal analysis protocols. IHC scores incorporated expression levels and percentages of positive cells. Digital and visual evaluation of membrane‐associated EpCAM yielded correlating scorings, whereas visual evaluation of nuclear Slug resulted in significantly higher overall scores. Multivariable Cox proportional hazard analysis defined the median EpCAM expression levels resulting from visual quantification as an independent prognostic factor of overall survival. Slug expression levels resulting from digital quantification were an independent prognostic factor of recurrence‐free survival, locoregional recurrence‐free survival, and disease‐specific survival. Hence, we propose to use visual assessment for the membrane‐associated EpCAM protein, whereas nuclear protein Slug assessment was more accurate following digital measurement.
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Affiliation(s)
- Henrik Schinke
- Department of Otorhinolaryngology, Head and Neck Surgery, Ludwig-Maximilians-University Munich, Germany
| | - Theresa Heider
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Timm Herkommer
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Florian Simon
- Department of Otorhinolaryngology, Head and Neck Surgery, Ludwig-Maximilians-University Munich, Germany
| | - Alexandra Blancke Soares
- Department of Otorhinolaryngology, Head and Neck Surgery, Ludwig-Maximilians-University Munich, Germany
| | - Gisela Kranz
- Department of Otorhinolaryngology, Head and Neck Surgery, Ludwig-Maximilians-University Munich, Germany
| | - Daniel Samaga
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Laura Dajka
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Annette Feuchtinger
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Axel Walch
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Laura Valeanu
- Institute of Pathology, Faculty of Medicine, LMU Munich, Germany
| | - Christoph Walz
- Institute of Pathology, Faculty of Medicine, LMU Munich, Germany
| | - Thomas Kirchner
- Institute of Pathology, Faculty of Medicine, LMU Munich, Germany
| | - Martin Canis
- Department of Otorhinolaryngology, Head and Neck Surgery, Ludwig-Maximilians-University Munich, Germany
| | - Philipp Baumeister
- Department of Otorhinolaryngology, Head and Neck Surgery, Ludwig-Maximilians-University Munich, Germany.,Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer", Helmholtz Zentrum München, Neuherberg, Germany
| | - Claus Belka
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer", Helmholtz Zentrum München, Neuherberg, Germany.,Department of Radiation Oncology, Ludwig-Maximilians-University Munich, Germany
| | - Cornelius Maihöfer
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer", Helmholtz Zentrum München, Neuherberg, Germany.,Department of Radiation Oncology, Ludwig-Maximilians-University Munich, Germany
| | - Sebastian Marschner
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer", Helmholtz Zentrum München, Neuherberg, Germany.,Department of Radiation Oncology, Ludwig-Maximilians-University Munich, Germany
| | - Ulrike Pflugradt
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer", Helmholtz Zentrum München, Neuherberg, Germany.,Department of Radiation Oncology, Ludwig-Maximilians-University Munich, Germany
| | - Ute Ganswindt
- Department of Therapeutic Radiology and Oncology, Medical University of Innsbruck, Austria
| | - Julia Hess
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, Neuherberg, Germany.,Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer", Helmholtz Zentrum München, Neuherberg, Germany
| | - Horst Zitzelsberger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, Neuherberg, Germany.,Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer", Helmholtz Zentrum München, Neuherberg, Germany
| | - Olivier Gires
- Department of Otorhinolaryngology, Head and Neck Surgery, Ludwig-Maximilians-University Munich, Germany.,Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer", Helmholtz Zentrum München, Neuherberg, Germany
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15
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Matzke LA, Watson PH. Biobanking for Cancer Biomarker Research: Issues and Solutions. Biomark Insights 2020; 15:1177271920965522. [PMID: 33192050 PMCID: PMC7594219 DOI: 10.1177/1177271920965522] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 09/17/2020] [Indexed: 12/31/2022] Open
Abstract
Biomarkers are critical tools that underpin precision medicine. However there has been slow progress and frequent failure of biomarker development. The root causes are multifactorial. Here, we focus on the need for fast, efficient, and reliable access to quality biospecimens as a critical area that impacts biomarker development. We discuss the past history of biobanking and the evolution of biobanking processes relevant to the specific area of cancer biomarker development as an example, and describe some solutions that can improve this area, thus potentially accelerating biomarker research.
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Affiliation(s)
- Lise A Matzke
- Office of Biobank Education and
Research, Department of Pathology and Laboratory Medicine, University of British
Columbia, Vancouver, British Columbia, Canada
- Biobanking and Biospecimen Research
Services, Deeley Research Centre, BC Cancer Agency, Victoria, British Columbia,
Canada
| | - Peter H Watson
- Office of Biobank Education and
Research, Department of Pathology and Laboratory Medicine, University of British
Columbia, Vancouver, British Columbia, Canada
- Biobanking and Biospecimen Research
Services, Deeley Research Centre, BC Cancer Agency, Victoria, British Columbia,
Canada
- Canadian Tissue Repository Network,
Vancouver, Canada
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16
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Hu Y, Mulot C, Bourreau C, Martin D, Laurent-Puig P, Radoï L, Guénel P, Borges CR. Biochemically Tracked Variability of Blood Plasma Thawed-State Exposure Times in a Multisite Collection Study. Biopreserv Biobank 2020; 18:376-388. [PMID: 32608993 PMCID: PMC9836705 DOI: 10.1089/bio.2019.0137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The integrity of blood plasma/serum (P/S) specimens can be impacted by preanalytical handling and storage conditions that result in thawed-state exposures (> -30°C). We recently reported a simple dilute-and-shoot, intact-protein liquid chromatography/mass spectrometry (LC/MS) assay called ΔS-Cys-Albumin that quantifies cumulative exposure of P/S to thawed conditions based on the change in relative abundance of the oxidized (S-cysteinylated) proteoform of albumin (S-Cys-Albumin) in the native sample to that of an aliquot of the sample intentionally driven to its maximum oxidation state. Herein, we evaluated the effect of prestorage delay and initial storage temperature on sample integrity by applying the ΔS-Cys-Albumin assay to a set of plasma samples (n = 413) collected under a single clinical study but from 12 different collection sites. Major differences (p < 0.0001) were observed between different groups of samples with modestly inconsistent initial handling conditions (i.e., initial processing of whole blood to plasma and placement at -80°C completed in under 3 hours, 3-13 hours, and over 17 hours). ΔS-Cys-Albumin was significantly inversely correlated with delay time at 4°C before centrifugation and total delay before final storage at -80°C (p < 0.0001). Samples from two collection sites had much lower ΔS-Cys-Albumin values relative to samples from other sites, in accordance with the fact that they were stored at -20°C for an average of 7.6 months before shipment to the central repository for final storage at -80°C. Based on the rate law for S-Cys-Albumin formation in plasma ex vivo, the average time that each plasma specimen had been exposed to the equivalent of room temperature (23°C) was back calculated from the measured ΔS-Cys-Albumin values. A survey of clinical analytes in P/S whose measured concentrations are sensitive to the initial handling/storage conditions documented in this study is provided and the ramifications of the plasma integrity findings from this multisite clinical study are discussed.
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Affiliation(s)
- Yueming Hu
- School of Molecular Sciences and The Biodesign Institute at Arizona State University, Tempe, Arizona, USA
| | - Claire Mulot
- INSERM, UMR-S 1147, CRB EPIGENETEC, Université Paris Descartes, Université Sorbonne Paris Cité, Paris, France
| | - Camille Bourreau
- INSERM, UMR-S 1147, CRB EPIGENETEC, Université Paris Descartes, Université Sorbonne Paris Cité, Paris, France
| | - Diane Martin
- INSERM, Center for Research in Epidemiology and Population Health (CESP), Cancer and Environment Team, Université Paris-Sud, Université Paris-Saclay, Villejuif, France
| | - Pierre Laurent-Puig
- INSERM, UMR-S 1147, CRB EPIGENETEC, Université Paris Descartes, Université Sorbonne Paris Cité, Paris, France
| | - Loredana Radoï
- INSERM, Center for Research in Epidemiology and Population Health (CESP), Cancer and Environment Team, Université Paris-Sud, Université Paris-Saclay, Villejuif, France.,Faculty of Dental Surgery, University Paris Descartes, Paris, France
| | - Pascal Guénel
- INSERM, Center for Research in Epidemiology and Population Health (CESP), Cancer and Environment Team, Université Paris-Sud, Université Paris-Saclay, Villejuif, France
| | - Chad R. Borges
- School of Molecular Sciences and The Biodesign Institute at Arizona State University, Tempe, Arizona, USA.,Address correspondence to: Chad R. Borges, PhD, School of Molecular Sciences, The Biodesign Institute at Arizona State University, P.O. Box 876401, Tempe, AZ 85287, USA
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17
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Dhondt B, Lumen N, De Wever O, Hendrix A. Preparation of Multi-omics Grade Extracellular Vesicles by Density-Based Fractionation of Urine. STAR Protoc 2020; 1:100073. [PMID: 33111109 PMCID: PMC7580105 DOI: 10.1016/j.xpro.2020.100073] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The multidimensional cargo of extracellular vesicles (EV) released in urine is a reflection of the pathophysiological processes occurring within their cells and tissues of origin in the urogenital system. Here, we describe a step-by-step protocol for density-based separation of urinary EV with high specificity and repeatability. The implementation of integrative omics allows the study of the molecular complexity of highly purified urinary EV, supporting the identification of EV-specific functions and biomarkers. For complete details on the use and execution of this protocol, please refer to Dhondt et al. (2020).
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Affiliation(s)
- Bert Dhondt
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Urology, Ghent University Hospital, Ghent, Belgium
| | - Nicolaas Lumen
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Urology, Ghent University Hospital, Ghent, Belgium
| | - Olivier De Wever
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - An Hendrix
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
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18
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Ng Kee Kwong KC, Gregory JM, Pal S, Chandran S, Mehta AR. Cerebrospinal fluid cytotoxicity in amyotrophic lateral sclerosis: a systematic review of in vitro studies. Brain Commun 2020; 2:fcaa121. [PMID: 33094283 PMCID: PMC7566327 DOI: 10.1093/braincomms/fcaa121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/17/2020] [Accepted: 07/22/2020] [Indexed: 12/11/2022] Open
Abstract
Various studies have suggested that a neurotoxic cerebrospinal fluid profile could be implicated in amyotrophic lateral sclerosis. Here, we systematically review the evidence for cerebrospinal fluid cytotoxicity in amyotrophic lateral sclerosis and explore its clinical correlates. We searched the following databases with no restrictions on publication date: PubMed, Embase and Web of Science. All studies that investigated cytotoxicity in vitro following exposure to cerebrospinal fluid from amyotrophic lateral sclerosis patients were considered for inclusion. Meta-analysis could not be performed, and findings were instead narratively summarized. Twenty-eight studies were included in our analysis. Both participant characteristics and study conditions including cerebrospinal fluid concentration, exposure time and culture model varied considerably across studies. Of 22 studies assessing cell viability relative to controls, 19 studies reported a significant decrease following exposure to cerebrospinal fluid from patients with amyotrophic lateral sclerosis, while three early studies failed to observe any difference. Seven of eight studies evaluating apoptosis observed significant increases in the levels of apoptotic markers following exposure to cerebrospinal fluid from patients with amyotrophic lateral sclerosis, with the remaining study reporting a qualitative difference. Although five studies investigated the possible relationship between cerebrospinal fluid cytotoxicity and patient characteristics, such as age, gender and disease duration, none demonstrated an association with any of the factors. In conclusion, our analysis suggests that cerebrospinal fluid cytotoxicity is a feature of sporadic and possibly also of familial forms of amyotrophic lateral sclerosis. Further research is, however, required to better characterize its underlying mechanisms and to establish its possible contribution to amyotrophic lateral sclerosis pathophysiology.
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Affiliation(s)
| | - Jenna M Gregory
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.,UK Dementia Research Institute at University of Edinburgh, Edinburgh, UK.,Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK.,MRC Edinburgh Brain Bank, Academic Department of Neuropathology, University of Edinburgh, Edinburgh, UK.,Edinburgh Pathology, University of Edinburgh, Edinburgh, UK
| | - Suvankar Pal
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.,Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK.,Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh, UK
| | - Siddharthan Chandran
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.,UK Dementia Research Institute at University of Edinburgh, Edinburgh, UK.,Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK.,Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh, UK.,Centre for Brain Development and Repair, inStem, Bangalore, India
| | - Arpan R Mehta
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.,UK Dementia Research Institute at University of Edinburgh, Edinburgh, UK.,Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK.,Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh, UK.,Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
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19
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Zabana Y, Lorén V, Domènech E, Aterido A, Garcia-Jaraquemada A, Julià A, Vicario M, Pedrosa E, Ferreiro M, Troya J, Lozano JJ, Sarrias MR, Cabré E, Mañosa M, Manyé J. Transcriptomic identification of TMIGD1 and its relationship with the ileal epithelial cell differentiation in Crohn's disease. Am J Physiol Gastrointest Liver Physiol 2020; 319:G109-G120. [PMID: 32508154 DOI: 10.1152/ajpgi.00027.2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Crohn's disease (CD) is a complex and multifactorial illness. There are still considerable gaps in our knowledge regarding its pathophysiology. A transcriptomic approach could shed some light on little-known biological alterations of the disease. We therefore aimed to explore the ileal transcriptome to gain knowledge about CD. We performed whole transcriptome gene expression analysis on ileocecal resections from CD patients and inflammatory bowel disease-free controls, as well as on a CD-independent cohort to replicate selected results. Normalized data were hierarchically clustered, and gene ontology and the molecular network were studied. Cell cultures and molecular methods were used for further evaluations. Genome-wide expression data analysis identified a robust transmembrane immunoglobulin domain-containing 1 (TMIGD1) gene underexpression in CD tissue, which was even more marked in inflamed ileum, and which was replicated in the validation cohort. Immunofluorescence showed TMIGD1 to be located in the apical microvilli of well-differentiated enterocytes but not in intestinal crypt. This apical TMIGD1 was lower in the noninflamed tissue and almost disappeared in the inflamed mucosa of surgical resections. In vitro studies showed hypoxic-dependent TMIGD1 decreased its expression in enterocyte-like cells. The gene enrichment analysis linked TMIGD1 with cell recovery and tissue remodeling in CD settings, involving guanylate cyclase activities. Transcriptomics may be useful for finding new targets that facilitate studies of the CD pathology. This is how TMIGD1 was identified in CD patients, which was related to multiciliate ileal epithelial cell differentiation.NEW & NOTEWORTHY This is a single-center translational research study that aimed to look for key targets involved in Crohn's disease and define molecular pathways through different functional analysis strategies. With this approach, we have identified and described a novel target, the almost unknown TMIGD1 gene, which may be key in the recovery of injured mucosa involving intestinal epithelial cell differentiation.
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Affiliation(s)
- Yamile Zabana
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain.,Centro de Investigación Biomédica en Red (CIBER), Madrid, Spain
| | - Violeta Lorén
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain.,Centro de Investigación Biomédica en Red (CIBER), Madrid, Spain
| | - Eugeni Domènech
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain.,Centro de Investigación Biomédica en Red (CIBER), Madrid, Spain.,Gastroenterology Department, Germans Trias i Pujol University Hospital, Badalona, Catalonia, Spain
| | - Adrià Aterido
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona, Catalonia, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Arce Garcia-Jaraquemada
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain
| | - Antonio Julià
- Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona, Catalonia, Spain
| | - Maria Vicario
- Centro de Investigación Biomédica en Red (CIBER), Madrid, Spain.,Laboratory of Translational Mucosal Immunology & Department of Gastroenterology, Digestive Diseases Research Unit, Vall d'Hebron Research University Hospital, Badalona, Catalonia, Spain
| | - Elisabet Pedrosa
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain
| | - Miriam Ferreiro
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain
| | - José Troya
- Colorectal Surgery Unit, General and Digestive Surgery Department, Germans Trias i Pujol University Hospital, Badalona, Catalonia, Spain
| | - Juan J Lozano
- Centro de Investigación Biomédica en Red (CIBER), Madrid, Spain
| | - Maria R Sarrias
- Centro de Investigación Biomédica en Red (CIBER), Madrid, Spain.,Innate Immunity Group, IGTP (AGAUR 2017-SGR-490 group), Badalona, Catalonia, Spain
| | - Eduard Cabré
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain.,Centro de Investigación Biomédica en Red (CIBER), Madrid, Spain.,Gastroenterology Department, Germans Trias i Pujol University Hospital, Badalona, Catalonia, Spain
| | - Miriam Mañosa
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain.,Centro de Investigación Biomédica en Red (CIBER), Madrid, Spain.,Gastroenterology Department, Germans Trias i Pujol University Hospital, Badalona, Catalonia, Spain
| | - Josep Manyé
- IBD Research Group, Germans Trias i Pujol Research Institute (IGTP), Badalona, Catalonia, Spain.,Centro de Investigación Biomédica en Red (CIBER), Madrid, Spain
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20
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Swift SL, Duffy S, Lang SH. Impact of tumor heterogeneity and tissue sampling for genetic mutation testing: a systematic review and post hoc analysis. J Clin Epidemiol 2020; 126:45-55. [PMID: 32540382 DOI: 10.1016/j.jclinepi.2020.06.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 06/10/2020] [Indexed: 02/07/2023]
Abstract
OBJECTIVE The objective of the study was to identify guidelines to assist systematic reviewers or clinical researchers in identifying sampling bias due to tumor heterogeneity (TH) in solid cancers assayed for somatic mutations. We also assessed current reporting standards to determine the impact of TH on sample bias. STUDY DESIGN AND SETTING We conducted a systematic review searching 13 databases (to January 2019) to identify guidelines. A post hoc analysis was performed using 12 prostate tumor somatic mutation data sets from a previous systematic review to assess reporting on TH. RESULTS Searches identified 2,085 records. No formal guidelines were identified. Forty publications contained incidental recommendations across five major themes: using multiple tumor samples (n = 29), sample purity thresholds (n = 14), using specific sequencing methods (n = 8), using liquid biopsies (n = 4), and microdissection (n = 4). In post hoc analyses, 50% (6 of 12) clearly reported pathology methods. Forty-two percent (5 of 12) did not report pathology results. Forty-two percent (5 of 12) confirmed the pathology of the sample by direct diagnosis rather than inference. Forty-two percent (5 of 12) used multiple samples per patient. Fifty-eight percent (7 of 12) reported on tumor purity (reported ranges 10% to 100%). CONCLUSIONS As precision medicine progresses to the clinic, guidelines are required to help evidence-based decision makers understand how TH may impact sample bias. Authors need to clearly report pathology methods and results and tumor purity methods and results.
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Affiliation(s)
| | - Steve Duffy
- Kleijnen Systematic Reviews Ltd, Escrick, York YO19 6FD, UK
| | - Shona H Lang
- Kleijnen Systematic Reviews Ltd, Escrick, York YO19 6FD, UK.
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21
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Lermen D, Gwinner F, Bartel-Steinbach M, Mueller SC, Habermann JK, Balwir MB, Smits E, Virgolino A, Fiddicke U, Berglund M, Åkesson A, Bergstrom A, Leander K, Horvat M, Snoj Tratnik J, Posada de la Paz M, Castaño Calvo A, Esteban López M, von Briesen H, Zimmermann H, Kolossa-Gehring M. Towards Harmonized Biobanking for Biomonitoring: A Comparison of Human Biomonitoring-Related and Clinical Biorepositories. Biopreserv Biobank 2020; 18:122-135. [PMID: 32281895 PMCID: PMC7185365 DOI: 10.1089/bio.2019.0092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Human biomonitoring (HBM) depends on high-quality human samples to identify status and trends in exposure and ensure comparability of results. In this context, much effort has been put into the development of standardized processes and quality assurance for sampling and chemical analysis, while effects of sample storage and shipment on sample quality have been less thoroughly addressed. To characterize the currently applied storage and shipment procedures within the consortium of the European Human Biomonitoring Initiative (HBM4EU), which aims at harmonization of HBM in Europe, a requirement analysis based on data from an online survey was conducted. In addition, the online survey was addressed to professionals in clinical biobanking represented by members of the European, Middle Eastern and African Society for Biopreservation and Biobanking (ESBB) to identify the current state-of-the-art in terms of sample storage and shipment. Results of this survey conducted in these two networks were compared to detect processes with potential for optimization and harmonization. In general, many similarities exist in sample storage and shipment procedures applied by ESBB members and HBM4EU partners and many requirements for ensuring sample quality are already met also by HBM4EU partners. Nevertheless, a need for improvement was identified for individual steps in sample storage, shipment, and related data management with potential impact on sample and data quality for HBM purposes. Based on these findings, recommendations for crucial first steps to further strengthen sample quality, and thus foster advancement in HBM on a pan-European level are given.
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Affiliation(s)
- Dominik Lermen
- Fraunhofer Institute for Biomedical Engineering IBMT, Biomonitoring & Biobanks, Sulzbach, Germany
- European, Middle Eastern & African Society for Biopreservation and Biobanking, Brussels, Belgium
- The European Human-Biomonitoring Initiative HBM4EU
| | - Frederik Gwinner
- Fraunhofer Institute for Biomedical Engineering IBMT, Biomonitoring & Biobanks, Sulzbach, Germany
- The European Human-Biomonitoring Initiative HBM4EU
| | - Martina Bartel-Steinbach
- Fraunhofer Institute for Biomedical Engineering IBMT, Biomonitoring & Biobanks, Sulzbach, Germany
- The European Human-Biomonitoring Initiative HBM4EU
| | - Sabine C. Mueller
- Fraunhofer Institute for Biomedical Engineering IBMT, Biomonitoring & Biobanks, Sulzbach, Germany
- The European Human-Biomonitoring Initiative HBM4EU
| | - Jens K. Habermann
- European, Middle Eastern & African Society for Biopreservation and Biobanking, Brussels, Belgium
- University Clinical Center Schleswig-Holstein, University of Luebeck, Translational Surgical Oncology and Biobanking, Luebeck, Germany
| | - Matharoo-Ball Balwir
- European, Middle Eastern & African Society for Biopreservation and Biobanking, Brussels, Belgium
- Nottingham University Hospital, Translational Research and Nottingham Health Science Biobank (NHSB), Nottingham, United Kingdom
| | - Elke Smits
- European, Middle Eastern & African Society for Biopreservation and Biobanking, Brussels, Belgium
- Antwerp University Hospital, University of Antwerp, Division of Medical Director, Edegem, Belgium
| | - Ana Virgolino
- The European Human-Biomonitoring Initiative HBM4EU
- Faculdade de Medicina, Instituto de Saúde Ambiental, Universidade de Lisboa, Lisboa, Portugal
| | - Ulrike Fiddicke
- The European Human-Biomonitoring Initiative HBM4EU
- German Environment Agency (Umweltbundesamt), Berlin, Germany
| | - Marika Berglund
- The European Human-Biomonitoring Initiative HBM4EU
- Institute of Environmental Medicine, Karolinska Institute, Institute of Environmental Medicine (IMM), Stockholm, Sweden
| | - Agneta Åkesson
- The European Human-Biomonitoring Initiative HBM4EU
- Institute of Environmental Medicine, Karolinska Institute, Institute of Environmental Medicine (IMM), Stockholm, Sweden
| | - Anna Bergstrom
- The European Human-Biomonitoring Initiative HBM4EU
- Institute of Environmental Medicine, Karolinska Institute, Institute of Environmental Medicine (IMM), Stockholm, Sweden
| | - Karin Leander
- The European Human-Biomonitoring Initiative HBM4EU
- Institute of Environmental Medicine, Karolinska Institute, Institute of Environmental Medicine (IMM), Stockholm, Sweden
| | - Milena Horvat
- The European Human-Biomonitoring Initiative HBM4EU
- Jožef Stefan Institute, Department of Environmental Sciences, Ljubljana, Slovenia
| | - Janja Snoj Tratnik
- The European Human-Biomonitoring Initiative HBM4EU
- Jožef Stefan Institute, Department of Environmental Sciences, Ljubljana, Slovenia
| | - Manuel Posada de la Paz
- The European Human-Biomonitoring Initiative HBM4EU
- Institute of Rare Diseases Research, CIBERER, EuroBiobanK, Instituto de Salud Carlos III, Madrid, Spain
| | - Argelia Castaño Calvo
- The European Human-Biomonitoring Initiative HBM4EU
- Centro Nacional de Sanidad Ambiental CNSA, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Marta Esteban López
- The European Human-Biomonitoring Initiative HBM4EU
- Centro Nacional de Sanidad Ambiental CNSA, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Hagen von Briesen
- Fraunhofer Institute for Biomedical Engineering IBMT, Biomonitoring & Biobanks, Sulzbach, Germany
- The European Human-Biomonitoring Initiative HBM4EU
| | - Heiko Zimmermann
- Fraunhofer Institute for Biomedical Engineering IBMT, Biomonitoring & Biobanks, Sulzbach, Germany
- The European Human-Biomonitoring Initiative HBM4EU
| | - Marike Kolossa-Gehring
- The European Human-Biomonitoring Initiative HBM4EU
- German Environment Agency (Umweltbundesamt), Berlin, Germany
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22
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Carsetti R, Di Sabatino A, Rosado MM, Cascioli S, Piano Mortari E, Milito C, Grimsholm O, Aranburu A, Giorda E, Tinozzi FP, Pulvirenti F, Donato G, Morini F, Bagolan P, Corazza GR, Quinti I. Lack of Gut Secretory Immunoglobulin A in Memory B-Cell Dysfunction-Associated Disorders: A Possible Gut-Spleen Axis. Front Immunol 2020; 10:2937. [PMID: 31969880 PMCID: PMC6960143 DOI: 10.3389/fimmu.2019.02937] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 11/29/2019] [Indexed: 12/23/2022] Open
Abstract
Background: B-1a B cells and gut secretory IgA (SIgA) are absent in asplenic mice. Human immunoglobulin M (IgM) memory B cells, which are functionally equivalent to mouse B-1a B cells, are reduced after splenectomy. Objective: To demonstrate whether IgM memory B cells are necessary for generating IgA-secreting plasma cells in the human gut. Methods: We studied intestinal SIgA in two disorders sharing the IgM memory B cell defect, namely asplenia, and common variable immune deficiency (CVID). Results: Splenectomy was associated with reduced circulating IgM memory B cells and disappearance of intestinal IgA-secreting plasma cells. CVID patients with reduced circulating IgM memory B cells had a reduced frequency of gut IgA+ plasma cells and a disrupted film of SIgA on epithelial cells. Toll-like receptor 9 (TLR9) and transmembrane activator and calcium-modulator and cyclophilin ligand interactor (TACI) induced IgM memory B cell differentiation into IgA+ plasma cells in vitro. In the human gut, TACI-expressing IgM memory B cells were localized under the epithelial cell layer where the TACI ligand a proliferation inducing ligand (APRIL) was extremely abundant. Conclusions: Circulating IgM memory B cell depletion was associated with a defect of intestinal IgA-secreting plasma cells in asplenia and CVID. The observation that IgM memory B cells have a distinctive role in mucosal protection suggests the existence of a functional gut-spleen axis.
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Affiliation(s)
- Rita Carsetti
- B Cell Pathophysiology Unit, IRCCS Bambino Gesù Children's Hospital, Rome, Italy.,Diagnostic Immunology Unit, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Antonio Di Sabatino
- First Department of Medicine, IRCCS San Matteo Hospital Foundation, University of Pavia, Pavia, Italy
| | - Maria Manuela Rosado
- B Cell Pathophysiology Unit, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Simona Cascioli
- B Cell Pathophysiology Unit, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Eva Piano Mortari
- B Cell Pathophysiology Unit, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Cinzia Milito
- Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - Ola Grimsholm
- B Cell Pathophysiology Unit, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Alaitz Aranburu
- B Cell Pathophysiology Unit, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Ezio Giorda
- B Cell Pathophysiology Unit, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Francesco Paolo Tinozzi
- Second Department of Surgery, IRCCS San Matteo Hospital Foundation, University of Pavia, Pavia, Italy
| | | | - Giuseppe Donato
- Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Francesco Morini
- Department of Medical and Surgical Neonatology, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Pietro Bagolan
- Department of Medical and Surgical Neonatology, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Gino Roberto Corazza
- First Department of Medicine, IRCCS San Matteo Hospital Foundation, University of Pavia, Pavia, Italy
| | - Isabella Quinti
- Department of Molecular Medicine, Sapienza University, Rome, Italy
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23
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Kelten Talu C, Toper MH, Şahin Y, Erdoğdu İH. Pathology and Biobanking. Turk Patoloji Derg 2020; 36:93-108. [PMID: 32189322 PMCID: PMC10511253 DOI: 10.5146/tjpath.2020.01482] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 02/23/2020] [Indexed: 11/18/2022] Open
Abstract
Biobanks are units where high quality and long-term protection of biomaterials is maintained. This system, in which biological materials and data are systematically recorded and stored, is a unique resource for the study of the pathophysiology of disease, the development of diagnostic biomarkers, and working with human tissues for the potential discovery of targeted therapeutic agents. At this point, the pathology unit plays a unifying and complementary role between the clinical and core disciplines and offers optimal management of the patients' biomaterials for diagnostic and research projects. The aim of this article is to present general information with regard to a biobank constructed for the storage of tumor tissue and blood biospecimens. Ethical issues (informed consent, protection of confidentiality and privacy, and secondary use of biospecimens) and the information technology system (collection, systematic recording, backup and protection of clinical information) are important issues in biobanking. The selection of freezers to be used in storage (mechanical freezers, liquid-vapor nitrogen tanks), and if mechanical freezers are preferred the establishment of the relevant infrastructure and support team (such as additional power units for protection from power outages), the preservation of materials by aliquoting in different freezers, ensuring financing so as to afford the cost of the infrastructure, and implementation of all these dynamics while adhering to international guidelines are of the utmost importance.
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Affiliation(s)
- Canan Kelten Talu
- Department of Molecular Pathology, Graduate School of Health Sciences, Dokuz Eylul University, Izmir, Turkey
| | - Muhammed Hasan Toper
- Department of Molecular Pathology, Graduate School of Health Sciences, Dokuz Eylul University, Izmir, Turkey
| | - Yasemin Şahin
- Department of Molecular Pathology, Graduate School of Health Sciences, Dokuz Eylul University, Izmir, Turkey
| | - İbrahim Halil Erdoğdu
- Department of Molecular Pathology, Graduate School of Health Sciences, Dokuz Eylul University, Izmir, Turkey
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24
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Pansare K, Pillai D, Parab S, Singh SR, Kannan S, Ludbe M, Hole A, Murali Krishna C, Gera P. Quality assessment of cryopreserved biospecimens reveals presence of intact biomolecules. JOURNAL OF BIOPHOTONICS 2019; 12:e201960048. [PMID: 31569303 DOI: 10.1002/jbio.201960048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/03/2019] [Accepted: 09/15/2019] [Indexed: 06/10/2023]
Abstract
Recapitulation of tumor features in isolated biomolecules is preeminently dependent on obtaining reliable quality biospecimen. Moreover, quality assessment of biobanked specimens at regular intervals is an essential intervention for carrying out effective translational and clinical research. In the current study, genomic DNA was extracted from 140 fresh frozen tissues of oral, breast and colorectal specimens cryopreserved over a period of 3 to 8 months (short term) and 3 to 4 years (long term). Quantification of genomic DNA by absorption and fluorescence spectroscopy confirmed high concentration while qualitative analysis by gel electrophoresis showed intact bands for 94% and 87% of short- and long-term cohorts, respectively. PC-LDA based classification of Raman spectra showed overlapping groups of both cohorts suggesting the quality of DNA being preserved irrespective of storage period. To the best of our knowledge this is the first Indian biobank study reporting quality analysis of biospecimens cryopreserved at different time periods.
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Affiliation(s)
| | - Divya Pillai
- Department of Biorepository, TMC, ACTREC, Mumbai, India
| | - Saili Parab
- Department of Biorepository, TMC, ACTREC, Mumbai, India
| | | | - Sadhana Kannan
- Clinical Trials Unit, Clinical Research Secretariat, TMC, ACTREC, Mumbai, India
| | - Madan Ludbe
- Department of Biorepository, TMC, ACTREC, Mumbai, India
| | - Arti Hole
- Chilakapati Lab, TMC, ACTREC, Mumbai, India
| | | | - Poonam Gera
- Department of Biorepository, TMC, ACTREC, Mumbai, India
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25
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Sidorenkov G, Nagel J, Meijer C, Duker JJ, Groen HJM, Halmos GB, Oonk MHM, Oostergo RJ, van der Vegt B, Witjes MJH, Nijland M, Havenga K, Maduro JH, Gietema JA, de Bock GH. The OncoLifeS data-biobank for oncology: a comprehensive repository of clinical data, biological samples, and the patient's perspective. J Transl Med 2019; 17:374. [PMID: 31727094 PMCID: PMC6857242 DOI: 10.1186/s12967-019-2122-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 10/31/2019] [Indexed: 11/25/2022] Open
Abstract
Background Understanding cancer heterogeneity, its temporal evolution over time, and the outcomes of guided treatment depend on accurate data collection in a context of routine clinical care. We have developed a hospital-based data-biobank for oncology, entitled OncoLifeS (Oncological Life Study: Living well as a cancer survivor), that links routine clinical data with preserved biological specimens and quality of life assessments. The aim of this study is to describe the organization and development of a data-biobank for cancer research. Results We have enrolled 3704 patients aged ≥ 18 years diagnosed with cancer, of which 45 with hereditary breast-ovarian cancer (70% participation rate) as of October 24th, 2019. The average age is 63.6 ± 14.2 years and 1892 (51.1%) are female. The following data are collected: clinical and treatment details, comorbidities, lifestyle, radiological and pathological findings, and long-term outcomes. We also collect and store various biomaterials of patients as well as information from quality of life assessments. Conclusion Embedding a data-biobank in clinical care can ensure the collection of high-quality data. Moreover, the inclusion of longitudinal quality of life data allows us to incorporate patients’ perspectives and inclusion of imaging data provides an opportunity for analyzing raw imaging data using artificial intelligence (AI) methods, thus adding new dimensions to the collected data.
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Affiliation(s)
- Grigory Sidorenkov
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Janny Nagel
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Coby Meijer
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jacko J Duker
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Harry J M Groen
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Gyorgy B Halmos
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Maaike H M Oonk
- Department of Obstetrics and Gynaecology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Rene J Oostergo
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Bert van der Vegt
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Max J H Witjes
- Department of Oral and Maxillofacial Surgery, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marcel Nijland
- Department of Haematology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Klaas Havenga
- Department of Surgery, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - John H Maduro
- Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jourik A Gietema
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Gertruida H de Bock
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
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26
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Iafolla MAJ, Picardo S, Aung K, Hansen AR. Systematic review and REMARK scoring of renal cell carcinoma prognostic circulating biomarker manuscripts. PLoS One 2019; 14:e0222359. [PMID: 31639128 PMCID: PMC6804962 DOI: 10.1371/journal.pone.0222359] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 08/27/2019] [Indexed: 12/19/2022] Open
Abstract
Background No validated molecular biomarkers exist to help guide prognosis of renal cell carcinoma (RCC) patients. We seek to evaluate the quality of published prognostic circulating RCC biomarker manuscripts using the Reporting Recommendations for Tumor Marker Prognostic Studies (REMARK) guidelines. Methods The phrase “(renal cell carcinoma OR renal cancer OR kidney cancer OR kidney carcinoma) AND circulating AND (biomarkers OR cell free DNA OR tumor DNA OR methylated cell free DNA OR methylated tumor DNA)” was searched in Embase, Medline and PubMed March 2018. Relevant manuscripts were scored using 48 REMARK sub-criteria for a maximal score of 20 points. Results The search identified 535 publications: 33 were manuscripts of primary research and were analyzed. The mean REMARK score was 10.6 (range 6.42–14.2). All manuscripts stated their biomarker, study objectives and method of case selection. The lowest scoring criteria: time lapse between storage of blood/serum and marker assay (n = 2) and lack of flow diagram (n = 2). REMARK scores were significantly higher in publications stating adherence to REMARK guidelines (p = 0.0307) and reporting statistically significant results (p = 0.0318). Conclusions Most RCC prognostic biomarker manuscripts poorly adhere to the REMARK guidelines. Better designed studies and appropriate reporting are required to address this urgent unmet need.
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Affiliation(s)
- Marco A. J. Iafolla
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- University of Toronto, Toronto, Ontario, Canada
| | - Sarah Picardo
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- University of Toronto, Toronto, Ontario, Canada
| | - Kyaw Aung
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- University of Toronto, Toronto, Ontario, Canada
- Livestrong Cancer Institute and Dell Medical School, University of Texas at Austin, Austin, Texas, United States of America
| | - Aaron R. Hansen
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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27
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Sreekumar R, Emaduddin M, Al-Saihati H, Moutasim K, Chan J, Spampinato M, Bhome R, Yuen HM, Mescoli C, Vitale A, Cillo U, Rugge M, Primrose J, Hilal MA, Thirdborough S, Tulchinsky E, Thomas G, Mirnezami A, Sayan AE. Protein kinase C inhibitors override ZEB1-induced chemoresistance in HCC. Cell Death Dis 2019; 10:703. [PMID: 31543517 PMCID: PMC6755133 DOI: 10.1038/s41419-019-1885-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 07/26/2019] [Indexed: 02/07/2023]
Abstract
Epithelial-mesenchymal transition (EMT) is a process by which tumour cells lose epithelial characteristics, become mesenchymal and highly motile. EMT pathways also induce stem cell features and resistance to apoptosis. Identifying and targeting this pool of tumour cells is a major challenge. Protein kinase C (PKC) inhibition has been shown to eliminate breast cancer stem cells but has never been assessed in hepatocellular cancer (HCC). We investigated ZEB family of EMT inducer expression as a biomarker for metastatic HCC and evaluated the efficacy of PKC inhibitors for HCC treatment. We showed that ZEB1 positivity predicted patient survival in multiple cohorts and also validated as an independent biomarker of HCC metastasis. ZEB1-expressing HCC cell lines became resistant to conventional chemotherapeutic agents and were enriched in CD44high/CD24low cell population. ZEB1- or TGFβ-induced EMT increased PKCα abundance. Probing public databases ascertained a positive association of ZEB1 and PKCα expression in human HCC tumours. Inhibition of PKCα activity by small molecule inhibitors or by PKCA knockdown reduced viability of mesenchymal HCC cells in vitro and in vivo. Our results suggest that ZEB1 expression predicts survival and metastatic potential of HCC. Chemoresistant/mesenchymal HCC cells become addicted to PKC pathway and display sensitivity to PKC inhibitors such as UCN-01. Stratifying patients according to ZEB1 and combining UCN-01 with conventional chemotherapy may be an advantageous chemotherapeutic strategy.
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Affiliation(s)
- Rahul Sreekumar
- University of Southampton Cancer Sciences Division, Somers Cancer Research Building, Southampton University, Tremona Road, Southampton, UK
- Department of Surgery, Southampton University Hospital NHS Trust, Southampton, UK
| | - Muhammad Emaduddin
- University of Southampton Cancer Sciences Division, Somers Cancer Research Building, Southampton University, Tremona Road, Southampton, UK
| | - Hajir Al-Saihati
- University of Southampton Cancer Sciences Division, Somers Cancer Research Building, Southampton University, Tremona Road, Southampton, UK
| | - Karwan Moutasim
- University of Southampton Cancer Sciences Division, Somers Cancer Research Building, Southampton University, Tremona Road, Southampton, UK
| | - James Chan
- University of Southampton Cancer Sciences Division, Somers Cancer Research Building, Southampton University, Tremona Road, Southampton, UK
| | - Marcello Spampinato
- HPB Unit, Department of General and Minimally Invasive Surgery, Policlinico of Abano Terme, Abano Terme, Italy
| | - Rahul Bhome
- University of Southampton Cancer Sciences Division, Somers Cancer Research Building, Southampton University, Tremona Road, Southampton, UK
- Department of Surgery, Southampton University Hospital NHS Trust, Southampton, UK
| | - Ho Ming Yuen
- Primary Care and Population Sciences, University of Southampton, Southampton, UK
| | | | - Alessandro Vitale
- Hepatobiliary and Liver Transplantation Unit, University of Padua, Padua, Italy
| | - Umberto Cillo
- Hepatobiliary and Liver Transplantation Unit, University of Padua, Padua, Italy
| | - Massimo Rugge
- Department of Pathology, University of Padua, Padua, Italy
| | - John Primrose
- University of Southampton Cancer Sciences Division, Somers Cancer Research Building, Southampton University, Tremona Road, Southampton, UK
- Department of Surgery, Southampton University Hospital NHS Trust, Southampton, UK
| | - Mohammad Abu Hilal
- Department of Surgery, Southampton University Hospital NHS Trust, Southampton, UK
| | - Stephen Thirdborough
- University of Southampton Cancer Sciences Division, Somers Cancer Research Building, Southampton University, Tremona Road, Southampton, UK
| | - Eugene Tulchinsky
- Cancer Sciences and Molecular Medicine Department, University of Leicester, Leicester, UK
- Moscow Institute of Physics and Technology, Dolgoprudnuy, Moscow region, Moscow, Russia
- Department of Biomedical Sciences, Nazarbayev University School of Medicine, Astana, Kazakhstan
| | - Gareth Thomas
- University of Southampton Cancer Sciences Division, Somers Cancer Research Building, Southampton University, Tremona Road, Southampton, UK
| | - Alex Mirnezami
- University of Southampton Cancer Sciences Division, Somers Cancer Research Building, Southampton University, Tremona Road, Southampton, UK
- Department of Surgery, Southampton University Hospital NHS Trust, Southampton, UK
| | - A Emre Sayan
- University of Southampton Cancer Sciences Division, Somers Cancer Research Building, Southampton University, Tremona Road, Southampton, UK.
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28
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Elshafay A, Omran ES, Abdelkhalek M, El-Badry MO, Eisa HG, Fala SY, Dang T, Ghanem MAT, Elbadawy M, Elhady MT, Vuong NL, Hirayama K, Huy NT. Reporting quality in systematic reviews of in vitro studies: a systematic review. Curr Med Res Opin 2019; 35:1631-1641. [PMID: 30977685 DOI: 10.1080/03007995.2019.1607270] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Background: Systematic reviews (SRs) and/or meta-analyses of in vitro research have an important role in establishing the foundation for clinical studies. In this study, we aimed to evaluate the reporting quality of SRs of in vitro studies using the PRISMA checklist.Method: Four databases were searched including PubMed, Virtual Health Library (VHL), Web of Science (ISI) and Scopus. The search was limited from 2006 to 2016 to include all SRs and/or meta-analyses (MAs) of pure in vitro studies. The evaluation of reporting quality was done using the PRISMA checklist.Results: Out of 7702 search results, 65 SRs were included and evaluated with the PRISMA checklist. Overall, the mean overall quality score of reported items of the PRISMA checklist was 68%. We have noticed an increasing pattern in the numbers of published SRs of in vitro studies over the last 10 years. In contrast, the reporting quality was not significantly improved over the same period (p = .363). There was a positive but not significant correlation between the overall quality score and the journal impact factor of the included studies.Conclusions: The adherence of SRs of in vitro studies to the PRISMA guidelines was poor. Therefore, we believe that using reporting guidelines and journals paying attention to this fact will improve the quality of SRs of in vitro studies.
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Affiliation(s)
- Abdelrahman Elshafay
- Faculty of Medicine, Al-Azhar University, Cairo, Egypt
- Online Research Club (http://www.onlineresearchclub.org/)
| | - Esraa Salah Omran
- Online Research Club (http://www.onlineresearchclub.org/)
- Kasralainy School of Medicine, Cairo University, Cairo, Egypt
| | - Mariam Abdelkhalek
- Online Research Club (http://www.onlineresearchclub.org/)
- Microbiology and Immunology Department, Faculty of Medicine, Tanta University, Tanta, Egypt
| | - Mohamed Omar El-Badry
- Faculty of Medicine, Al-Azhar University, Cairo, Egypt
- Online Research Club (http://www.onlineresearchclub.org/)
| | - Heba Gamal Eisa
- Online Research Club (http://www.onlineresearchclub.org/)
- Faculty of Medicine, Menoufia University, Shebin El-Kom, Egypt
| | - Salma Y Fala
- Online Research Club (http://www.onlineresearchclub.org/)
- Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Thao Dang
- Online Research Club (http://www.onlineresearchclub.org/)
- Surgery Department School of Medicine, Tan Tao University, Tan Duc Ecity, Vietnam
| | - Mohammad A T Ghanem
- Online Research Club (http://www.onlineresearchclub.org/)
- Department of Vascular Surgery, Uniklinik Magdeburg, Magdeburg, Germany
| | - Maha Elbadawy
- Online Research Club (http://www.onlineresearchclub.org/)
- Ministry of Health, Cairo, Egypt
| | - Mohamed Tamer Elhady
- Online Research Club (http://www.onlineresearchclub.org/)
- Department of Pediatrics, Zagazig University Hospitals, Faculty of Medicine, Sharkia, Egypt
| | - Nguyen Lam Vuong
- Online Research Club (http://www.onlineresearchclub.org/)
- Department of Medical Statistics and Informatics, Faculty of Public Health, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Kenji Hirayama
- Department of Immunogenetics, Institute of Tropical Medicine (NEKKEN), Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Nguyen Tien Huy
- Evidence Based Medicine Research Group & Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Department of Clinical Product Development, Institute of Tropical Medicine (NEKKEN), School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
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29
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Lang SH, Swift SL, White H, Misso K, Kleijnen J, Quek RG. A systematic review of the prevalence of DNA damage response gene mutations in prostate cancer. Int J Oncol 2019; 55:597-616. [PMID: 31322208 PMCID: PMC6685596 DOI: 10.3892/ijo.2019.4842] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 06/28/2019] [Indexed: 02/06/2023] Open
Abstract
Several ongoing international prostate cancer (PC) clinical trials are exploring therapies that target the DNA damage response (DDR) pathway. This systematic review summarizes the prevalence of DDR mutation carriers in the unselected (general) PC and familial PC populations. A total of 11 electronic databases, 10 conference proceedings, and grey literature sources were searched from their inception to December 2017. Studies reporting the prevalence of somatic and/or germline DDR mutations were summarized. Metastatic PC (mPC), castration‑resistant PC (CRPC) and metastatic CRPC (mCRPC) subgroups were included. A total of 11,648 records were retrieved, and 80 studies (103 records) across all PC populations were included; 59 records were of unselected PC and 13 records of familial PC. Most data were available for DDR panels (n=12 studies), ataxia telangiectasia mutated (ATM; n=13), breast cancer susceptibility gene (BRCA)1 (n=14) and BRCA2 (n=20). ATM, BRCA2 and partner and localizer of BRCA2 (PALB2) had the highest mutation rates (≥4%). Median prevalence rates for DDR germline mutations were 18.6% in PC (range, 17.2‑19%; three studies, n=1,712), 11.6% in mPC (range, 11.4‑11.8%; two studies, n=1,261) and 8.3% in mCRPC (range, 7.5‑9.1%; two studies, n=738). Median prevalence rates for DDR somatic mutations were 10.7% in PC (range, 4.9‑22%; three studies, n=680), 13.2% in mPC (range, 10‑16.4%; two studies, n=105) and not reported (NR) in mCRPC. The prevalence of DDR germline and/or somatic mutations was 27% in PC (one study, n=221), 22.67% in mCRPC (one study, n=150) and NR in mPC. In familial PC, median mutation prevalence was 12.1% (range, 7.3‑16.9%) for germline DDR (two studies, n=315) and 3.7% (range, 1.3‑7.9%) for BRCA2 (six studies, n=945). In total, 88% of studies were at a high risk of bias. The prevalence of DDR gene mutations in PC varied widely within somatic subgroups depending on study size, genetic screening techniques, DDR mutation definition and PC diagnosis; somatic and/or germline DDR mutation prevalence was in the range of 23‑27% in PC. These findings support DDR mutation testing for all patients with PC (including those with mCRPC). With the advent of the latest clinical practice PC guidelines highlighting the importance of DDR mutation screening, and ongoing mCRPC clinical trials evaluating DDR mutation‑targeted drugs, future larger epidemiological studies are warranted to further quantify the international burden of DDR mutations in PC.
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Affiliation(s)
| | | | | | - Kate Misso
- Information Department, Kleijnen Systematic Reviews Ltd., Escrick, York YO19 6FD, UK
| | - Jos Kleijnen
- Reviews Department
- School for Public Health and Primary Care, Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - Ruben G.W. Quek
- Health Economics and Outcomes Research, Pfizer Inc., San Francisco, CA 94105, USA
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30
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Gedye C, Sachchithananthan M, Leonard R, Jeffree RL, Buckland ME, Ziegler DS, Graeber MB, Day BW, McDonald KL, Lasocki A, Nowak AK. Driving innovation through collaboration: development of clinical annotation datasets for brain cancer biobanking. Neurooncol Pract 2019; 7:31-37. [PMID: 32257282 DOI: 10.1093/nop/npz036] [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: 11/14/2022] Open
Abstract
Background A key component of cancer research is the availability of clinical samples with appropriately annotated clinical data. Biobanks facilitate research by collecting/storing various types of clinical samples for research. Brain Cancer Biobanking Australia (BCBA) was established to facilitate the networking of brain cancer biobanking operations Australia-wide. Maximizing biospecimen utility in a networked biobanking environment requires the standardization of procedures and data across different sites. The aim of this research was to scope and develop a recommended clinical annotation dataset both for pediatric and adult brain cancer biobanks. Methods A multidisciplinary working group consisting of members from the BCBA Consortium was established to develop clinical dataset recommendations for brain cancer biobanks. A literature search was undertaken to identify any published clinical dataset recommendations for brain cancer biobanks. An audit of data items collected and stored by BCBA member biobanks was also conducted to survey current clinical data collection practices across the BCBA network. Results BCBA has developed a clinical annotation dataset recommendation for pediatric and adult brain cancer biobanks. The clinical dataset recommendation has 5 clinical data categories: demographic, clinical and radiological diagnosis and surgery, neuropathological diagnosis, patient treatment, and patient follow-up. The data fields have been categorized into 1 of 3 tiers; essential, preferred, and comprehensive. This enables biobanks and researchers to prioritize appropriately where resources are limited. Conclusion This dataset can be used to guide the integration of data from multiple existing biobanks for research studies and for planning prospective brain cancer biobanking activities.
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Affiliation(s)
- Craig Gedye
- Brain Cancer Biobanking Australia, National Health and Medical Research Council Clinical Trials Centre, The University of Sydney, NSW, Australia.,Clinical Research Director, NSW Health Statewide Biobank, Camperdown NSW.,School of Medicine and Public Health, University of Newcastle, Callaghan, NSW, Australia.,Calvary Mater Newcastle, Waratah, NSW, Australia
| | - Mythily Sachchithananthan
- Brain Cancer Biobanking Australia, National Health and Medical Research Council Clinical Trials Centre, The University of Sydney, NSW, Australia
| | - Robyn Leonard
- Brain Cancer Biobanking Australia, National Health and Medical Research Council Clinical Trials Centre, The University of Sydney, NSW, Australia
| | - Rosalind L Jeffree
- Brain Cancer Biobanking Australia, National Health and Medical Research Council Clinical Trials Centre, The University of Sydney, NSW, Australia.,Royal Brisbane and Women's Hospital, University of Queensland, Australia
| | - Michael E Buckland
- Brain Cancer Biobanking Australia, National Health and Medical Research Council Clinical Trials Centre, The University of Sydney, NSW, Australia.,Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia.,Discipline of Pathology, Brain & Mind Centre, University of Sydney, NSW, Australia
| | - David S Ziegler
- Brain Cancer Biobanking Australia, National Health and Medical Research Council Clinical Trials Centre, The University of Sydney, NSW, Australia.,Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia.,School of Women's and Children's Health, University of New South Wales, Sydney, Australia.,Children's Cancer Institute, University of New South Wales, Sydney, Australia
| | - Manuel B Graeber
- Brain Cancer Biobanking Australia, National Health and Medical Research Council Clinical Trials Centre, The University of Sydney, NSW, Australia.,Brain Tumor Research Laboratories, Brain and Mind Centre, The University of Sydney, NSW, Australia
| | - Bryan W Day
- Brain Cancer Biobanking Australia, National Health and Medical Research Council Clinical Trials Centre, The University of Sydney, NSW, Australia.,QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Kerrie L McDonald
- Brain Cancer Biobanking Australia, National Health and Medical Research Council Clinical Trials Centre, The University of Sydney, NSW, Australia.,Cure Brain Cancer Neuro-oncology Laboratory, Prince of Wales Clinical School, University of New South Wales, Sydney, Australia.,Prince of Wales Clinical School, University of New South Wales, Sydney, Australia
| | - Arian Lasocki
- Brain Cancer Biobanking Australia, National Health and Medical Research Council Clinical Trials Centre, The University of Sydney, NSW, Australia.,Department of Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Victoria.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | | | - Anna K Nowak
- Brain Cancer Biobanking Australia, National Health and Medical Research Council Clinical Trials Centre, The University of Sydney, NSW, Australia.,School of Medicine and Pharmacology, University of Western Australia, Crawley.,Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands, Australia
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Meredith AJ, Simeon-Dubach D, Matzke LA, Cheah S, Watson PH. Biospecimen Data Reporting in the Research Literature. Biopreserv Biobank 2019; 17:326-333. [DOI: 10.1089/bio.2018.0143] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Anna J. Meredith
- Office of Biobank Education and Research, Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | | | - Lise A. Matzke
- Office of Biobank Education and Research, Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Stefanie Cheah
- Office of Biobank Education and Research, Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Peter H. Watson
- Office of Biobank Education and Research, Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
- Tumour Tissue Repository, Deeley Research Centre, BC Cancer Agency, Victoria, Canada
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Linsen L, T'Joen V, Van Der Straeten C, Van Landuyt K, Marbaix E, Bekaert S, Ectors N. Biobank Quality Management in the BBMRI.be Network. Front Med (Lausanne) 2019; 6:141. [PMID: 31294024 PMCID: PMC6606712 DOI: 10.3389/fmed.2019.00141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/07/2019] [Indexed: 01/20/2023] Open
Abstract
From as early as 2005, different guidelines and quality standards covering biobank activities and sample handling methods have been developed to improve and guarantee the reproducibility of biomarker research. Ten years on, the BBMRI.be Quality working group wanted to gauge the current situation of these aspects in the biobanks of the BBMRI.be network. To this end, two online surveys were launched (fall 2017 and fall 2018) to the biobank quality managers in the BBMRI.be network to determine the status and setup of their current quality management system (QMS) and how their QMS and related practices have evolved over a 14 month time period. All biobanks addressed by the two surveys provided a complete response (12 and 13, respectively). A QMS was implemented in 85% of biobanks, with 4 standards emerging as primary basis. Supplementary guidelines were used, with a strong preference for the ISBER best practices for biobanks. The Standard Preanalytical Code—an indicator of the preanalytical lifecycle of a biospecimen impacting the downstream analysis results—was already implemented in 50% of the biobanks while the other half intends future implementation. To assess and maintain the quality of their QMS, 62% of biobanks used self-assessment tools and 71% participated in proficiency testing schemes. The majority of biobanks had implemented procedures for general and biobank specific activities. However, policies regarding the business and sustainability aspect of biobank were only implemented in a limited number of biobanks. A clear desire for a peer-review audit was expressed by 69% of biobanks, with over half of them intending to implement the recently published biobank standard ISO20387. Overall, the biobanks of the BBMRI.be network have actively implemented a solid quality approach in their practices. The implementation of ISO 20387 may bring further professionalization of activities. Based on the needs expressed in this survey, the Quality working group will be setting up an audit program for the BBMRI.be biobanks, to enhance, harmonize and streamline their activities. On the whole, the biobanks in the BBMRI.be network are able to substantially contribute to translational research, as a primary facilitator guaranteeing high quality standards and reproducibility.
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Affiliation(s)
- Loes Linsen
- Biobank, University Hospitals Leuven, Leuven, Belgium
| | - Veronique T'Joen
- Bioresource Center Ghent, Health Innovation and Research Institute, University Hospital Ghent, Ghent, Belgium
| | - Catherine Van Der Straeten
- Bioresource Center Ghent, Health Innovation and Research Institute, University Hospital Ghent, Ghent, Belgium
| | | | - Etienne Marbaix
- Pathology Department, de Duve Institute, Saint-Luc University Clinics, Catholic University of Louvain, Brussels, Belgium
| | - Sofie Bekaert
- Department of Public Health and Primary Care, Faculty for Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Nadine Ectors
- Biobank, University Hospitals Leuven, Leuven, Belgium
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LaBaer J, Miceli JF, Freedman LP. What's in a sample? Increasing transparency in biospecimen procurement methods. Nat Methods 2019; 15:303-304. [PMID: 29702632 DOI: 10.1038/nmeth.4684] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Joshua LaBaer
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Joseph F Miceli
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
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Hall PS, Mitchell ED, Smith AF, Cairns DA, Messenger M, Hutchinson M, Wright J, Vinall-Collier K, Corps C, Hamilton P, Meads D, Lewington A. The future for diagnostic tests of acute kidney injury in critical care: evidence synthesis, care pathway analysis and research prioritisation. Health Technol Assess 2019; 22:1-274. [PMID: 29862965 DOI: 10.3310/hta22320] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Acute kidney injury (AKI) is highly prevalent in hospital inpatient populations, leading to significant mortality and morbidity, reduced quality of life and high short- and long-term health-care costs for the NHS. New diagnostic tests may offer an earlier diagnosis or improved care, but evidence of benefit to patients and of value to the NHS is required before national adoption. OBJECTIVES To evaluate the potential for AKI in vitro diagnostic tests to enhance the NHS care of patients admitted to the intensive care unit (ICU) and identify an efficient supporting research strategy. DATA SOURCES We searched ClinicalTrials.gov, The Cochrane Library databases, Embase, Health Management Information Consortium, International Clinical Trials Registry Platform, MEDLINE, metaRegister of Current Controlled Trials, PubMed and Web of Science databases from their inception dates until September 2014 (review 1), November 2015 (review 2) and July 2015 (economic model). Details of databases used for each review and coverage dates are listed in the main report. REVIEW METHODS The AKI-Diagnostics project included horizon scanning, systematic reviewing, meta-analysis of sensitivity and specificity, appraisal of analytical validity, care pathway analysis, model-based lifetime economic evaluation from a UK NHS perspective and value of information (VOI) analysis. RESULTS The horizon-scanning search identified 152 potential tests and biomarkers. Three tests, Nephrocheck® (Astute Medical, Inc., San Diego, CA, USA), NGAL and cystatin C, were subjected to detailed review. The meta-analysis was limited by variable reporting standards, study quality and heterogeneity, but sensitivity was between 0.54 and 0.92 and specificity was between 0.49 and 0.95 depending on the test. A bespoke critical appraisal framework demonstrated that analytical validity was also poorly reported in many instances. In the economic model the incremental cost-effectiveness ratios ranged from £11,476 to £19,324 per quality-adjusted life-year (QALY), with a probability of cost-effectiveness between 48% and 54% when tests were compared with current standard care. LIMITATIONS The major limitation in the evidence on tests was the heterogeneity between studies in the definitions of AKI and the timing of testing. CONCLUSIONS Diagnostic tests for AKI in the ICU offer the potential to improve patient care and add value to the NHS, but cost-effectiveness remains highly uncertain. Further research should focus on the mechanisms by which a new test might change current care processes in the ICU and the subsequent cost and QALY implications. The VOI analysis suggested that further observational research to better define the prevalence of AKI developing in the ICU would be worthwhile. A formal randomised controlled trial of biomarker use linked to a standardised AKI care pathway is necessary to provide definitive evidence on whether or not adoption of tests by the NHS would be of value. STUDY REGISTRATION The systematic review within this study is registered as PROSPERO CRD42014013919. FUNDING The National Institute for Health Research Health Technology Assessment programme.
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Affiliation(s)
- Peter S Hall
- Edinburgh Cancer Research Centre, University of Edinburgh, Edinburgh, UK
| | | | - Alison F Smith
- Academy of Primary Care, Hull York Medical School, Hull, UK.,National Institute for Health Research (NIHR) Diagnostic Evidence Co-operative Leeds, Leeds, UK
| | - David A Cairns
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | - Michael Messenger
- National Institute for Health Research (NIHR) Diagnostic Evidence Co-operative Leeds, Leeds, UK
| | | | - Judy Wright
- Academy of Primary Care, Hull York Medical School, Hull, UK
| | | | | | - Patrick Hamilton
- Manchester Institute of Nephrology and Transplantation, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - David Meads
- Academy of Primary Care, Hull York Medical School, Hull, UK
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Rizner TL, Adamski J. Paramount importance of sample quality in pre-clinical and clinical research-Need for standard operating procedures (SOPs). J Steroid Biochem Mol Biol 2019; 186:1-3. [PMID: 30261262 DOI: 10.1016/j.jsbmb.2018.09.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Tea Lanisnik Rizner
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia.
| | - Jerzy Adamski
- Helmholtz Zentrum München, Research Unit of Molecular Endocrinology and Metabolism, 85764 Neuherberg, Germany; German Centre for Diabetes Research (DZD), Neuherberg, Germany; Lehrstuhl für Experimentelle Genetik, Technische Universität München, Freising-Weihenstephan, Germany
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Onco-omics Approaches and Applications in Clinical Trials for Cancer Patients. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1168:79-90. [DOI: 10.1007/978-3-030-24100-1_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Jarczak J, Lach J, Borówka P, Gałka M, Bućko M, Marciniak B, Strapagiel D. BioSCOOP - Biobank Sample Communication Protocol. New approach for the transfer of information between biobanks. Database (Oxford) 2019; 2019:baz105. [PMID: 31609452 PMCID: PMC6791335 DOI: 10.1093/database/baz105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/06/2019] [Accepted: 08/02/2019] [Indexed: 02/02/2023]
Abstract
Dynamic development of biobanking industry (both business and science) resulted in an increased number of IT systems for samples and data management. The most difficult and complicated case for the biobanking community was cooperation between institutions, equipped with different IT systems, in the field of scientific research, mainly data interchange and information flow. Tools available on the market relate mainly to the biobank or collection level. Efficient and universal protocols including the detailed information about the donor and the sample are still very limited. Here, we have developed BioSCOOP, a communication protocol in the form of a well documented JSON API. The main aim of this study was to harmonize and standardize the rules of communication between biobanks on the level of information about the donor together with information about the sample. The purpose was to create a communication protocol for two applications: to transfer the information between different biobanks and to allow the searching and presentation of the sample and data sets.
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Affiliation(s)
- J Jarczak
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
- BBMRI.pl Consortium, Wrocław, Poland
| | - J Lach
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
- BBMRI.pl Consortium, Wrocław, Poland
| | - P Borówka
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | | | - M Bućko
- Bee2code sp. z o.o., ul. Daszyńskiego 5; 44-100 Gliwice
| | - B Marciniak
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
- BBMRI.pl Consortium, Wrocław, Poland
| | - D Strapagiel
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
- BBMRI.pl Consortium, Wrocław, Poland
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Kempf E, de Beyer JA, Cook J, Holmes J, Mohammed S, Nguyên TL, Simera I, Trivella M, Altman DG, Hopewell S, Moons KGM, Porcher R, Reitsma JB, Sauerbrei W, Collins GS. Overinterpretation and misreporting of prognostic factor studies in oncology: a systematic review. Br J Cancer 2018; 119:1288-1296. [PMID: 30353050 PMCID: PMC6251031 DOI: 10.1038/s41416-018-0305-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Cancer prognostic biomarkers have shown disappointing clinical applicability. The objective of this study was to classify and estimate how study results are overinterpreted and misreported in prognostic factor studies in oncology. METHODS This systematic review focused on 17 oncology journals with an impact factor above 7. PubMed was searched for primary clinical studies published in 2015, evaluating prognostic factors. We developed a classification system, focusing on three domains: misleading reporting (selective, incomplete reporting, misreporting), misleading interpretation (unreliable statistical analysis, spin) and misleading extrapolation of the results (claiming irrelevant clinical applicability, ignoring uncertainty). RESULTS Our search identified 10,844 articles. The 98 studies included investigated a median of two prognostic factors (Q1-Q3, 1-7). The prognostic factors' effects were selectively and incompletely reported in 35/98 and 24/98 full texts, respectively. Twenty-nine articles used linguistic spin in the form of strong statements. Linguistic spin rejecting non-significant results was found in 34 full-text results and 15 abstract results sections. One in five articles had discussion and/or abstract conclusions that were inconsistent with the study findings. Sixteen reports had discrepancies between their full-text and abstract conclusions. CONCLUSIONS Our study provides evidence of frequent overinterpretation of findings of prognostic factor assessment in high-impact medical oncology journals.
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Affiliation(s)
- Emmanuelle Kempf
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK
- Department of Medical Oncology, Henri Mondor and Albert Chenevier Teaching Hospital, APHP, Créteil, France
| | - Jennifer A de Beyer
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK
| | - Jonathan Cook
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK
| | - Jane Holmes
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK
| | - Seid Mohammed
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK
| | - Tri-Long Nguyên
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK
- Laboratory UPRES EA2415, Biostatistics, Epidemiology, Clinical Research and Health Economics, University of Montpellier, Montpellier, France
| | - Iveta Simera
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Marialena Trivella
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK
| | - Douglas G Altman
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK
| | - Sally Hopewell
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK
| | - Karel G M Moons
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Cochrane Netherlands, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Raphael Porcher
- Department of Epidemiology, Hôtel Dieu Teaching Hospital, APHP, Paris, France
| | - Johannes B Reitsma
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Cochrane Netherlands, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Willi Sauerbrei
- Institute for Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Gary S Collins
- Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, OX3 9DU, UK.
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High Expression of EpCAM and Sox2 is a Positive Prognosticator of Clinical Outcome for Head and Neck Carcinoma. Sci Rep 2018; 8:14582. [PMID: 30275505 PMCID: PMC6167386 DOI: 10.1038/s41598-018-32178-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 08/29/2018] [Indexed: 01/06/2023] Open
Abstract
Locally advanced head and neck squamous cell carcinomas (HNSCC) have limited prognosis due to frequent treatment failure. Currently, TNM-classification and human papillomavirus (HPV) infection are the sole clinical prognosticators of outcome. Tumor heterogeneity and stemness based on epithelial-mesenchymal-transition reportedly associate with therapy resistance. The capacity of epithelial marker EpCAM (EpEX), stemness regulator Sox2 and mesenchymal marker vimentin to predict clinical outcome of HSNCC patients was assessed upon immunohistochemistry staining in two cohorts of HNSCC patients treated with surgery and adjuvant radio (chemo) therapy (n = 94) and primary radio (chemo) therapy (n = 94), respectively. Prognostic values with respect to overall, disease-free and disease-specific survival were assessed in uni- and multivariate cox proportional hazard models to generate integrated risk scores. EpEX, Sox2 and vimentin displayed substantial inter- and intratumoral heterogeneity. EpEXhigh and Sox2high predicted improved clinical outcome in the discovery cohort and in the HPV-negative sub-cohort. EpEXhigh and Sox2high were confirmed as prognosticators of clinical outcome in the validation cohort treated with definitive radio(chemo)therapy. Importantly, EpEXhigh identified patients with improved survival within the HPV-negative subgroup of the validation cohort. Hence, Sox2high and particularly EpEXhigh have potential as tools to predict clinical performance of HNSCC patients, foremost HPV-negative cases, in the frame of molecular-guided treatment decision-making.
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Brunius C, Pedersen A, Malmodin D, Karlsson BG, Andersson LI, Tybring G, Landberg R. Prediction and modeling of pre-analytical sampling errors as a strategy to improve plasma NMR metabolomics data. Bioinformatics 2018; 33:3567-3574. [PMID: 29036400 PMCID: PMC5870544 DOI: 10.1093/bioinformatics/btx442] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/13/2017] [Indexed: 11/12/2022] Open
Abstract
Motivation Biobanks are important infrastructures for life science research. Optimal sample handling regarding e.g. collection and processing of biological samples is highly complex, with many variables that could alter sample integrity and even more complex when considering multiple study centers or using legacy samples with limited documentation on sample management. Novel means to understand and take into account such variability would enable high-quality research on archived samples. Results This study investigated whether pre-analytical sample variability could be predicted and reduced by modeling alterations in the plasma metabolome, measured by NMR, as a function of pre-centrifugation conditions (1–36 h pre-centrifugation delay time at 4 °C and 22 °C) in 16 individuals. Pre-centrifugation temperature and delay times were predicted using random forest modeling and performance was validated on independent samples. Alterations in the metabolome were modeled at each temperature using a cluster-based approach, revealing reproducible effects of delay time on energy metabolism intermediates at both temperatures, but more pronounced at 22 °C. Moreover, pre-centrifugation delay at 4 °C resulted in large, specific variability at 3 h, predominantly of lipids. Pre-analytical sample handling error correction resulted in significant improvement of data quality, particularly at 22 °C. This approach offers the possibility to predict pre-centrifugation delay temperature and time in biobanked samples before use in costly downstream applications. Moreover, the results suggest potential to decrease the impact of undesired, delay-induced variability. However, these findings need to be validated in multiple, large sample sets and with analytical techniques covering a wider range of the metabolome, such as LC-MS. Availability and implementation The sampleDrift R package is available at https://gitlab.com/CarlBrunius/sampleDrift. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Carl Brunius
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.,Department of Molecular Sciences, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden
| | - Anders Pedersen
- Swedish NMR Centre, University of Gothenburg, SE-405?30 Gothenburg, Sweden
| | - Daniel Malmodin
- Swedish NMR Centre, University of Gothenburg, SE-405?30 Gothenburg, Sweden
| | - B Göran Karlsson
- Swedish NMR Centre, University of Gothenburg, SE-405?30 Gothenburg, Sweden
| | | | | | - Rikard Landberg
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.,Department of Molecular Sciences, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden.,Institute of Environmental Medicine, Karolinska Institutet, SE-171 77 Stockholm, Sweden
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Andreasen S, Tan Q, Agander TK, Steiner P, Bjørndal K, Høgdall E, Larsen SR, Erentaite D, Olsen CH, Ulhøi BP, von Holstein SL, Wessel I, Heegaard S, Homøe P. Adenoid cystic carcinomas of the salivary gland, lacrimal gland, and breast are morphologically and genetically similar but have distinct microRNA expression profiles. Mod Pathol 2018; 31:1211-1225. [PMID: 29467480 DOI: 10.1038/s41379-018-0005-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 11/20/2017] [Accepted: 11/23/2017] [Indexed: 12/13/2022]
Abstract
Adenoid cystic carcinoma is among the most frequent malignancies in the salivary and lacrimal glands and has a grave prognosis characterized by frequent local recurrences, distant metastases, and tumor-related mortality. Conversely, adenoid cystic carcinoma of the breast is a rare type of triple-negative (estrogen and progesterone receptor, HER2) and basal-like carcinoma, which in contrast to other triple-negative and basal-like breast carcinomas has a very favorable prognosis. Irrespective of site, adenoid cystic carcinoma is characterized by gene fusions involving MYB, MYBL1, and NFIB, and the reason for the different clinical outcomes is unknown. In order to identify the molecular mechanisms underlying the discrepancy in clinical outcome, we characterized the phenotypic profiles, pattern of gene rearrangements, and global microRNA expression profiles of 64 salivary gland, 9 lacrimal gland, and 11 breast adenoid cystic carcinomas. All breast and lacrimal gland adenoid cystic carcinomas had triple-negative and basal-like phenotypes, while salivary gland tumors were indeterminate in 13% of cases. Aberrations in MYB and/or NFIB were found in the majority of cases in all three locations, whereas MYBL1 involvement was restricted to tumors in the salivary gland. Global microRNA expression profiling separated salivary and lacrimal gland adenoid cystic carcinoma from their respective normal glands but could not distinguish normal breast adenoid cystic carcinoma from normal breast tissue. Hierarchical clustering separated adenoid cystic carcinomas of salivary gland origin from those of the breast and placed lacrimal gland carcinomas in between these. Functional annotation of the microRNAs differentially expressed between salivary gland and breast adenoid cystic carcinoma showed these as regulating genes involved in metabolism, signal transduction, and genes involved in other cancers. In conclusion, microRNA dysregulation is the first class of molecules separating adenoid cystic carcinoma according to the site of origin. This highlights a novel venue for exploring the biology of adenoid cystic carcinoma.
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Affiliation(s)
- Simon Andreasen
- Department of Otorhinolaryngology and Maxillofacial Surgery, Zealand University Hospital, Køge, Denmark. .,Department of Otorhinolaryngology Head and Neck Surgery and Audiology, Rigshospitalet, Copenhagen, Denmark.
| | - Qihua Tan
- Department of Clinical Research, Unit of Human Genetics, University of Southern Denmark, Odense, Denmark
| | | | - Petr Steiner
- Department of Pathology, Faculty of Medicine, Charles University in Prague, Pilsen, Czech Republic.,Bioptic Laboratory Ltd, Molecular Pathology Laboratory, Pilsen, Czech Republic
| | - Kristine Bjørndal
- Department of ORL-Head and Neck Surgery, Odense University Hospital, Odense, Denmark
| | - Estrid Høgdall
- Department of Pathology, Herlev Hospital, University of Copenhagen, Herlev, Denmark
| | | | - Daiva Erentaite
- Department of Pathology, Aalborg University Hospital, Aalborg, Denmark
| | | | | | - Sarah Linéa von Holstein
- Department of Ophthalmology, Rigshospitalet-Glostrup, Copenhagen, Denmark.,Department of Ophthalmology, Zealand University Hospital, Roskilde, Denmark
| | - Irene Wessel
- Department of Otorhinolaryngology Head and Neck Surgery and Audiology, Rigshospitalet, Copenhagen, Denmark
| | - Steffen Heegaard
- Department of Pathology, Rigshospitalet, Copenhagen, Denmark.,Department of Ophthalmology, Rigshospitalet-Glostrup, Copenhagen, Denmark
| | - Preben Homøe
- Department of Otorhinolaryngology and Maxillofacial Surgery, Zealand University Hospital, Køge, Denmark
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Andreasen S, Tan Q, Agander TK, Hansen TVO, Steiner P, Bjørndal K, Høgdall E, Larsen SR, Erentaite D, Olsen CH, Ulhøi BP, Heegaard S, Wessel I, Homøe P. MicroRNA dysregulation in adenoid cystic carcinoma of the salivary gland in relation to prognosis and gene fusion status: a cohort study. Virchows Arch 2018; 473:329-340. [DOI: 10.1007/s00428-018-2423-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/20/2018] [Accepted: 07/22/2018] [Indexed: 01/14/2023]
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43
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Munsterman ID, Kendall TJ, Khelil N, Popa M, Lomme R, Drenth JPH, Tjwa ETTL. Extracellular matrix components indicate remodelling activity in different fibrosis stages of human non-alcoholic fatty liver disease. Histopathology 2018; 73:612-621. [PMID: 29856896 DOI: 10.1111/his.13665] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/30/2018] [Indexed: 01/18/2023]
Abstract
AIMS The composition of several important extracellular matrix components (ECM) has not yet been elucidated in human non-alcoholic fatty liver disease (NAFLD). We aim to investigate the proportion of hepatic stellate cells (HSCs) and activity of matrix metalloproteinases (MMPs) and tissue inhibitors of MMPs (TIMPs) in human NAFLD liver tissue with respect to severity of inflammation and fibrosis. METHODS AND RESULTS Histopathological features were quantified by NAFLD activity score and grading assignment. The collagen proportionate area (CPA) was measured. Slides were stained with alpha-smooth muscle actin (α-SMA), as a marker of activated HSCs, and α-SMA was quantified digitally. Zymography was performed to measure the proteolytic activity of MMP-2 and MMP-9. TIMP-1 and TIMP-2 protein concentration was measured with enzyme-linked immunosorbent assay (ELISA). α-SMA was higher in severe fibrosis (6.3%, interquartile range 2.9-13.1) than mild and no fibrosis (median 1.1 and 0.9%, P < 0.001) and correlated strongly with CPA (Rs = 0.870, P < 0.001). ProMMP-2 activity in severe (4.1%, IQR 2.6-16.2) and mild fibrosis (2.7%, IQR 1.9-3.9) was higher than in no fibrosis (1.5%, (IQR 0.95-2.1); P = 0.001 and P = 0.046) and showed a moderate positive correlation with CPA (Rs = 0.495, P = 0.001). TIMP-1 and TIMP-2 were significantly higher in severe fibrosis than mild or no fibrosis. Both showed moderate correlation with CPA (TIMP-1: Rs = 0.471, P = 0.002 and TIMP-2: Rs = 0.325, P = 0.036). MMP-9 correlated as the only ECM component to inflammation severity. CONCLUSIONS Advanced human NAFLD-fibrosis has a distinct ECM composition with increased HSCs and increased TIMP inhibition, but there is also ongoing remodelling activity of MMP-2.
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Affiliation(s)
- Isabelle D Munsterman
- Department of Gastroenterology and Hepatology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | | | - Nawel Khelil
- Department of Gastroenterology and Hepatology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Madalina Popa
- Department of Gastroenterology and Hepatology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Roger Lomme
- Laboratory of Experimental Surgery, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Joost P H Drenth
- Department of Gastroenterology and Hepatology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Eric T T L Tjwa
- Department of Gastroenterology and Hepatology, Radboud University Medical Centre, Nijmegen, the Netherlands
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Andreasen S. Molecular features of adenoid cystic carcinoma with an emphasis on microRNA expression. APMIS 2018; 126 Suppl 140:7-57. [DOI: 10.1111/apm.12828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Simon Andreasen
- Department of Otorhinolaryngology and Maxillofacial Surgery; Zealand University Hospital; Køge Denmark
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Christensen R, Heitmann BL, Andersen KW, Nielsen OH, Sørensen SB, Jawhara M, Bygum A, Hvid L, Grauslund J, Wied J, Glerup H, Fredberg U, Villadsen JA, Kjær SG, Fallingborg J, Moghadd SAGR, Knudsen T, Brodersen J, Frøjk J, Dahlerup JF, Bojesen AB, Sorensen GL, Thiel S, Færgeman NJ, Brandslund I, Bennike TB, Stensballe A, Schmidt EB, Franke A, Ellinghaus D, Rosenstiel P, Raes J, Boye M, Werner L, Nielsen CL, Munk HL, Nexøe AB, Ellingsen T, Holmskov U, Kjeldsen J, Andersen V. Impact of red and processed meat and fibre intake on treatment outcomes among patients with chronic inflammatory diseases: protocol for a prospective cohort study of prognostic factors and personalised medicine. BMJ Open 2018; 8:e018166. [PMID: 29439003 PMCID: PMC5829767 DOI: 10.1136/bmjopen-2017-018166] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
INTRODUCTION Chronic inflammatory diseases (CIDs) are frequently treated with biological medications, specifically tumour necrosis factor inhibitors (TNFi)). These medications inhibit the pro-inflammatory molecule TNF alpha, which has been strongly implicated in the aetiology of these diseases. Up to one-third of patients do not, however, respond to biologics, and lifestyle factors are assumed to affect treatment outcomes. Little is known about the effects of dietary lifestyle as a prognostic factor that may enable personalised medicine. The primary outcome of this multidisciplinary collaborative study will be to identify dietary lifestyle factors that support optimal treatment outcomes. METHODS AND ANALYSIS This prospective cohort study will enrol 320 patients with CID who are prescribed a TNFi between June 2017 and March 2019. Included among the patients with CID will be patients with inflammatory bowel disease (Crohn's disease and ulcerative colitis), rheumatic disorders (rheumatoid arthritis, axial spondyloarthritis, psoriatic arthritis), inflammatory skin diseases (psoriasis, hidradenitis suppurativa) and non-infectious uveitis. At baseline (pretreatment), patient characteristics will be assessed using patient-reported outcome measures, clinical assessments of disease activity, quality of life and lifestyle, in addition to registry data on comorbidity and concomitant medication(s). In accordance with current Danish standards, follow-up will be conducted 14-16 weeks after treatment initiation. For each disease, evaluation of successful treatment response will be based on established primary and secondary endpoints, including disease-specific core outcome sets. The major outcome of the analyses will be to detect variability in treatment effectiveness between patients with different lifestyle characteristics. ETHICS AND DISSEMINATION The principle goal of this project is to improve the quality of life of patients suffering from CID by providing evidence to support dietary and other lifestyle recommendations that may improve clinical outcomes. The study is approved by the Ethics Committee (S-20160124) and the Danish Data Protecting Agency (2008-58-035). Study findings will be disseminated through peer-reviewed journals, patient associations and presentations at international conferences. TRIAL REGISTRATION NUMBER NCT03173144; Pre-results.
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Affiliation(s)
- Robin Christensen
- Musculoskeletal Statistics Unit, The Parker Institute, Bispebjerg and Frederiksberg Hospital, Denmark
| | - Berit L Heitmann
- Research Unit for Dietary Studies, The Parker Institute, Bispebjerg and Frederiksberg Hospital, Denmark
- Section for General Medicine, Department of Public Health, University of Copenhagen, Denmark
- National Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - Karina Winther Andersen
- Focused Research Unit for Molecular Diagnostic and Clinical Research, IRS-Center Sonderjylland, Hospital of Southern Jutland, Aabenraa, Denmark
- Organ Centre, Hospital of Southern Jutland, Aabenraa, Denmark
| | - Ole Haagen Nielsen
- Department of Gastroenterology D112, Herlev Hospital, University of Copenhagen, Herlev, Denmark
| | - Signe Bek Sørensen
- Focused Research Unit for Molecular Diagnostic and Clinical Research, IRS-Center Sonderjylland, Hospital of Southern Jutland, Aabenraa, Denmark
- Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Mohamad Jawhara
- Focused Research Unit for Molecular Diagnostic and Clinical Research, IRS-Center Sonderjylland, Hospital of Southern Jutland, Aabenraa, Denmark
- Organ Centre, Hospital of Southern Jutland, Aabenraa, Denmark
- institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Anette Bygum
- Department of Dermatology and Allergy Centre, Odense University Hospital, Odense, Denmark
| | - Lone Hvid
- Department of Dermatology and Allergy Centre, Odense University Hospital, Odense, Denmark
| | - Jakob Grauslund
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- Department of Ophthalmology, Odense University Hospital, Odense, Denmark
| | - Jimmi Wied
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- Department of Ophthalmology, Odense University Hospital, Odense, Denmark
| | - Henning Glerup
- Diagnostic Centre, Silkeborg Regional Hospital, Silkeborg, Denmark
| | - Ulrich Fredberg
- Diagnostic Centre, Silkeborg Regional Hospital, Silkeborg, Denmark
- Department of Rheumatology, Odense University Hospital, Odense, Denmark
| | | | - Søren Geill Kjær
- Diagnostic Centre, Silkeborg Regional Hospital, Silkeborg, Denmark
| | - Jan Fallingborg
- Department of Gastroenterology and Hepatology, Aalborg University Hospital, Aalborg, Denmark
| | - Seyed A G R Moghadd
- Department of Internal Medicine, Herning Regional Hospital, Herning, Denmark
| | - Torben Knudsen
- Department of Gastroenterology, Hospital of Southwest Jutland, Esbjerg, Denmark
| | - Jacob Brodersen
- Department of Gastroenterology, Hospital of Southwest Jutland, Esbjerg, Denmark
| | - Jesper Frøjk
- Department of Gastroenterology, Hospital of Southwest Jutland, Esbjerg, Denmark
| | - Jens Frederik Dahlerup
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, Denmark
| | - Anders Bo Bojesen
- Focused Research Unit for Molecular Diagnostic and Clinical Research, IRS-Center Sonderjylland, Hospital of Southern Jutland, Aabenraa, Denmark
| | - Grith Lykke Sorensen
- Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Steffen Thiel
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Nils J Færgeman
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Ivan Brandslund
- institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
- Department of Clinical Biochemistry, Lillebaelt Hospital, Vejle, Denmark
| | - Tue Bjerg Bennike
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Allan Stensballe
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Erik Berg Schmidt
- Department of Cardiology, Aalborg University Hospital, Ålborg, Denmark
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Jeroen Raes
- Departmentof Microbiology and Immunology, Rega Institute, KU Leuven—University of Leuven, Leuven, Belgium
- VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Mette Boye
- Focused Research Unit for Molecular Diagnostic and Clinical Research, IRS-Center Sonderjylland, Hospital of Southern Jutland, Aabenraa, Denmark
| | - Lars Werner
- The Danish Psoriasis Association, The Danish Psoriasis Association, Tåstrup, Denmark
| | | | - Heidi Lausten Munk
- Diagnostic Centre, Silkeborg Regional Hospital, Silkeborg, Denmark
- Department of Rheumatology, Odense University Hospital, Odense, Denmark
| | | | - Torkell Ellingsen
- Diagnostic Centre, Silkeborg Regional Hospital, Silkeborg, Denmark
- Department of Rheumatology, Odense University Hospital, Odense, Denmark
| | - Uffe Holmskov
- Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Jens Kjeldsen
- Department of Gastroenterology, Odense University Hospital, Odense, Denmark
| | - Vibeke Andersen
- Focused Research Unit for Molecular Diagnostic and Clinical Research, IRS-Center Sonderjylland, Hospital of Southern Jutland, Aabenraa, Denmark
- Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
- institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
- OPEN, University of Southern Denmark, Odense, Denmark
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Cost-Effective Organization of an Institutional Human Cancer Biobank in a Clinical Setting: CRO-Biobank Experience Toward Harmonization. Int J Biol Markers 2018; 30:e243-51. [DOI: 10.5301/jbm.5000138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2014] [Indexed: 12/21/2022]
Abstract
This report describes the organization of the Biobank of the CRO Aviano National Cancer Institute, Aviano (CRO- Biobank), Italy, implemented as a structured facility dedicated to collecting human biological samples. It describes a particular disease-specific biobank and the integration of a research biobank in a clinical setting. The CRO-Biobank's mission is rooted in supporting and implementing cancer research, with its main focus on optimizing technical and quality processes, while also investigating ethical, legal and IT topics. The CRO-Biobank has implemented processes aimed at guaranteeing the safety of the providers, protecting patient privacy and ensuring both the traceability and quality of its samples. Our 8 years of experience allow us to offer insights and useful suggestions that may solve theoretical and practical issues that can arise when starting up new biobanks or developing existing biobanks further.
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Malczewska A, Kidd M, Matar S, Kos-Kudla B, Modlin IM. A Comprehensive Assessment of the Role of miRNAs as Biomarkers in Gastroenteropancreatic Neuroendocrine Tumors. Neuroendocrinology 2018; 107:73-90. [PMID: 29566385 DOI: 10.1159/000487326] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/25/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND/AIMS A key issue in neuroendocrine neoplasia management is the identification of blood signatures that specifically define the activity of a cancer or local tumor microenvironment. MicroRNAs (miRNAs) may represent such a candidate. To evaluate their clinical utility as biomarkers in gastroenteropancreatic neuroendocrine tumors (GEP-NETs), we assessed their expression in tissue and blood. METHODS A systematic review of PubMed was undertaken to identify studies investigating miRNAs in GEP-NETs and their utility as blood or tissue biomarkers. RESULTS Twenty-two studies using a range of methodologies with different normalization protocols were identified: tumor - gastric NET type 1 (n = 1 study: MiR-222, regulates p27KIP1), pancreatic (n = 6: MiR-21 [inflammatory marker, oncogene] and MiR-144 [PI3K/AKT signaling], both up- and downregulated depending on the method), small intestinal (n = 7: no consistent signature), and colorectal (n = 3: no consistent signature); blood - gastric NET type 1 (n = 1: MiR-222), pancreatic (n = 3: MiR-21), and small intestinal (n = 3: no consistent signature). The studies all included heterogeneous cohorts, were insufficiently powered, and utilized different methodologies, and age- and gender-matched controls were not used. Different miRNA isolation methods and detection protocols resulted in inconsistent expression comparing tumor and blood. A scientific discrepancy was the downregulated expression of some circulating candidates compared to tissue levels, suggesting methodological issues or physiological responses to the tumor. Both are of concern in defining the biometrics of a marker. CONCLUSIONS A potential biomarker for GEP-NETs included MiR-21 (small bowel and pancreas), but this epithelial tumor marker requires prospective validation. Overall, significant scientific investigation remains to identify and demonstrate neuroendocrine specificity and to validate candidate miRNA biomarkers.
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Affiliation(s)
- Anna Malczewska
- Department of Endocrinology and Neuroendocrine Tumors, Medical University of Silesia, Katowice, Poland
| | - Mark Kidd
- Wren Laboratories, Branford, Connecticut, USA
| | - Somer Matar
- Wren Laboratories, Branford, Connecticut, USA
| | - Beata Kos-Kudla
- Department of Endocrinology and Neuroendocrine Tumors, Medical University of Silesia, Katowice, Poland
| | - Irvin M Modlin
- Yale University School of Medicine, New Haven, Connecticut, USA
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Agrawal L, Engel KB, Greytak SR, Moore HM. Understanding preanalytical variables and their effects on clinical biomarkers of oncology and immunotherapy. Semin Cancer Biol 2017; 52:26-38. [PMID: 29258857 DOI: 10.1016/j.semcancer.2017.12.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/07/2017] [Accepted: 12/13/2017] [Indexed: 12/20/2022]
Abstract
Identifying a suitable course of immunotherapy treatment for a given patient as well as monitoring treatment response is heavily reliant on biomarkers detected and quantified in blood and tissue biospecimens. Suboptimal or variable biospecimen collection, processing, and storage practices have the potential to alter clinically relevant biomarkers, including those used in cancer immunotherapy. In the present review, we summarize effects reported for immunologically relevant biomarkers and highlight preanalytical factors associated with specific analytical platforms and assays used to predict and gauge immunotherapy response. Given that many of the effects introduced by preanalytical variability are gene-, transcript-, and protein-specific, biospecimen practices should be standardized and validated for each biomarker and assay to ensure accurate results and facilitate clinical implementation of newly identified immunotherapy approaches.
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Affiliation(s)
- Lokesh Agrawal
- Biorepositories and Biospecimen Research Branch (BBRB), Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Drive, Bethesda, Maryland, USA
| | | | | | - Helen M Moore
- Biorepositories and Biospecimen Research Branch (BBRB), Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Drive, Bethesda, Maryland, USA.
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Andeen NK, Bowman R, Baullinger T, Brooks JM, Tretiakova MS. Epitope Preservation Methods for Tissue Microarrays: Longitudinal Prospective Study. Am J Clin Pathol 2017; 148:380-389. [PMID: 29106459 DOI: 10.1093/ajcp/aqx062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES We sought to test recent guidelines for preserving immunoreactivity of precut slides, to quantify loss of immunoreactivity, and to determine potential for preservation by altering storage conditions. METHODS Precut slides from tissue microarrays were stored under one of several conditions: exposed to ambient air at room temperature, 4°C, or -20°C or in a vacuum-sealed container at room temperature, -20°C, -80°C, or with paraffin coating. At multiple intervals over 1 year, slides were stained with antibodies against p53, isocitrate dehydrogenase 1, Ki-67, synaptophysin, and androgen receptor and evaluated. RESULTS Compared with time 0, the overall median percentage immunoreactivity was 66% at 6 months and 51% at 1 year. During the experiment, this was as low as 55% for precut slides stored in paraffin coating and up to 87% for those stored at -20°C. Vacuum sealing was an effective preservative for some antibody targets and detrimental for others. Storage at -80°C did not have added value. CONCLUSIONS For precut slides, there is a time, storage condition, and antibody-dependent loss of immunoreactivity that could compromise analysis of prognostic, predictive, and diagnostic markers. Our findings support previous recommendations and suggest that the best storage conditions are at -20°C, without paraffin coating or vacuum sealing.
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Affiliation(s)
- Nicole K Andeen
- From the Department of Pathology, University of Washington, Seattle
| | - Regina Bowman
- From the Department of Pathology, University of Washington, Seattle
| | - Toni Baullinger
- From the Department of Pathology, University of Washington, Seattle
| | - J Mathew Brooks
- From the Department of Pathology, University of Washington, Seattle
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CD74 and intratumoral immune response in breast cancer. Oncotarget 2017; 8:12664-12674. [PMID: 27058619 PMCID: PMC5355043 DOI: 10.18632/oncotarget.8610] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 03/18/2016] [Indexed: 12/31/2022] Open
Abstract
CD74 (invariant chain) plays a role in MHC class II antigen presentation. We assessed CD74 and MHCII expression in tumor cells, as well as CD8, CD4, and CD68 tumor infiltrating leucocyte (TIL) density by immunohistochemistry in a cohort of 492 breast cancer patients. CD74 expression was associated with poor prognostic markers including patient age, tumor grade, ER status, non-Luminal A subtypes, and with MHCII expression and higher TIL densities, particularly in the Basal-like subgroup. Univariate analysis showed a favorable prognostic effect of CD74 (Hazard ratio = 0.46, 95% CI = 0.26–0.89, p = 0.022) and for combined CD74/MHCII (Hazard ratio = 0.26, 95% CI = 0.17–0.81, p = 0.014) positive status for overall survival that was only manifested in the Basal-like subgroup. CD74 and MHCII expression is associated with patient survival in Basal-like breast cancer, and the association with TIL may reflect an effective intratumoral immune response.
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