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Alkhatib R, Gaede KI. Data Management in Biobanking: Strategies, Challenges, and Future Directions. BIOTECH 2024; 13:34. [PMID: 39311336 PMCID: PMC11417763 DOI: 10.3390/biotech13030034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 08/23/2024] [Accepted: 08/31/2024] [Indexed: 09/26/2024] Open
Abstract
Biobanking plays a pivotal role in biomedical research by providing standardized processing, precise storing, and management of biological sample collections along with the associated data. Effective data management is a prerequisite to ensure the integrity, quality, and accessibility of these resources. This review provides a current landscape of data management in biobanking, discussing key challenges, existing strategies, and potential future directions. We explore multiple aspects of data management, including data collection, storage, curation, sharing, and ethical considerations. By examining the evolving technologies and methodologies in biobanking, we aim to provide insights into addressing the complexities and maximizing the utility of biobank data for research and clinical applications.
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Affiliation(s)
- Ramez Alkhatib
- Biomaterial Bank Nord, Research Center Borstel Leibniz Lung Center, Parkallee 35, 23845 Borstel, Germany;
- German Centre for Lung Research (DZL), Airway Research Centre North (ARCN), 22927 Großhansdorf, Germany
| | - Karoline I. Gaede
- Biomaterial Bank Nord, Research Center Borstel Leibniz Lung Center, Parkallee 35, 23845 Borstel, Germany;
- German Centre for Lung Research (DZL), Airway Research Centre North (ARCN), 22927 Großhansdorf, Germany
- PopGen 2.0 Biobanking Network (P2N), University Hospital Schleswig-Holstein, Campus Kiel, Kiel University, 24105 Kiel, Germany
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2
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Capasso E, Casella C, Marisei M, Tortora M, Briganti F, Di Lorenzo P. Imaging biobanks: operational limits, medical-legal and ethical reflections. Front Digit Health 2024; 6:1408619. [PMID: 39268200 PMCID: PMC11391398 DOI: 10.3389/fdgth.2024.1408619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 08/05/2024] [Indexed: 09/15/2024] Open
Abstract
The extraordinary growth of health technologies has determined an increasing interest in biobanks that represent a unique wealth for research, experimentation, and validation of new therapies. "Human" biobanks are repositories of various types of human biological samples. Through years the paradigm has shifted from spontaneous collections of biological material all over the world to institutional, organized, and well-structured forms. Imaging biobanks represent a novel field and are defined by European Society of Radiology as: "organized databases of medical images, and associated imaging biomarkers shared among multiple researchers, linked to other biorepositories". Modern radiology and nuclear medicine can provide multiple imaging biomarkers, that express the phenotype related to certain diseases, especially in oncology. Imaging biobanks, not a mere catalogue of bioimages associated to clinical data, involve advanced computer technologies to implement the emergent field of radiomics and radiogenomics. Since Europe hosts most of the biobanks, juridical and ethical framework, with a specific referral to Italy, is analyzed. Linking imaging biobanks to traditional ones appears to be a crucial step that needs to be driven by medical imaging community under clear juridical and ethical guidelines.
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Affiliation(s)
- Emanuele Capasso
- Department of Advanced Biomedical Sciences, University of Naples Federico II, Naples, Italy
| | - Claudia Casella
- Department of Advanced Biomedical Sciences, University of Naples Federico II, Naples, Italy
| | - Mariagrazia Marisei
- Department of Advanced Biomedical Sciences, University of Naples Federico II, Naples, Italy
| | - Mario Tortora
- Department of Advanced Biomedical Sciences, University of Naples Federico II, Naples, Italy
| | - Francesco Briganti
- Department of Advanced Biomedical Sciences, University of Naples Federico II, Naples, Italy
| | - Pierpaolo Di Lorenzo
- Department of Advanced Biomedical Sciences, University of Naples Federico II, Naples, Italy
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3
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Graham M, Samuel G, Farley M. Roadmap for low-carbon ultra-low temperature storage in biobanking. J Transl Med 2024; 22:747. [PMID: 39118108 PMCID: PMC11308585 DOI: 10.1186/s12967-024-05383-5] [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: 04/17/2024] [Accepted: 06/07/2024] [Indexed: 08/10/2024] Open
Abstract
Biobanks have become an integral part of health and bioscience research. However, the ultra-low temperature (ULT) storage methods that biobanks employ [ULT freezers and liquid nitrogen (LN2)] are associated with carbon emissions that contribute to anthropogenic climate change. This paper aims to provide a 'Roadmap' for reducing carbon emissions associated with ULT storage in biobanking. The Roadmap offers recommendations associated with nine areas of ULT storage practice: four relating to ULT freezers, three associated with LN2 storage, and two generalised discussions regarding biosample management and centralisation. For each practice, we describe (a) the best approaches to mitigate carbon emissions, (b) explore barriers associated with hindering their implementation, and (c) make a series of recommendations that can help biobank stakeholders overcome these barriers. The recommendations were the output of a one year, UK-based, multidisciplinary research project that involved a quantitative Carbon Footprinting Assessment of the emissions associated with 1 year of ULT storage (for both freezers and LN2) at four different case study sites; as well as two follow up stakeholder workshops to qualitatively explore UK biobank stakeholder perceptions, views, and experiences on how to consider such assessments within the broader social, political, financial, technical, and cultural contexts of biobanking.
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Affiliation(s)
- Matthew Graham
- Department for Global Health and Social Medicine, King's College London, London, WC2R 2LS, UK
| | - Gabrielle Samuel
- Department for Global Health and Social Medicine, King's College London, London, WC2R 2LS, UK.
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Pallocca M, Betti M, Baldinelli S, Palombo R, Bucci G, Mazzarella L, Tonon G, Ciliberto G. Clinical bioinformatics desiderata for molecular tumor boards. Brief Bioinform 2024; 25:bbae447. [PMID: 39297878 PMCID: PMC11411775 DOI: 10.1093/bib/bbae447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 06/28/2024] [Accepted: 08/30/2024] [Indexed: 09/26/2024] Open
Abstract
Clinical Bioinformatics is a knowledge framework required to interpret data of medical interest via computational methods. This area became of dramatic importance in precision oncology, fueled by cancer genomic profiling: most definitions of Molecular Tumor Boards require the presence of bioinformaticians. However, all available literature remained rather vague on what are the specific needs in terms of digital tools and expertise to tackle and interpret genomics data to assign novel targeted or biomarker-driven targeted therapies to cancer patients. To fill this gap, in this article, we present a catalog of software families and human skills required for the tumor board bioinformatician, with specific examples of real-world applications associated with each element presented.
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Affiliation(s)
- Matteo Pallocca
- Institute of Experimental Endocrinology and Oncology, National Research Council, Via Sergio Pansini, 5, 80131 Naples, Italy
| | - Martina Betti
- Biostatistics, Bioinformatics and Clinical Trial Center, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi, 53, 00144 Rome, Italy
| | - Sara Baldinelli
- Biostatistics, Bioinformatics and Clinical Trial Center, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi, 53, 00144 Rome, Italy
| | - Ramona Palombo
- Institute of Experimental Endocrinology and Oncology, National Research Council, Via Sergio Pansini, 5, 80131 Naples, Italy
| | - Gabriele Bucci
- Center for OMICS Sciences, IRCCS San Raffaele Scientific Institute, Via Olgettina, 60, 20132 Milan, Italy
| | - Luca Mazzarella
- Division of Gastrointestinal Medical Oncology and Neuroendocrine Tumors, IRCCS IEO - European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
- Department of Experimental Oncology, IRCCS IEO - European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Giovanni Tonon
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, and Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Via Olgettina, 60, 20132 Milan, Italy
| | - Gennaro Ciliberto
- Scientific Direction, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi, 53, 00144 Rome, Italy
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Monette A, Warren S, Barrett JC, Garnett-Benson C, Schalper KA, Taube JM, Topp B, Snyder A. Biomarker development for PD-(L)1 axis inhibition: a consensus view from the SITC Biomarkers Committee. J Immunother Cancer 2024; 12:e009427. [PMID: 39032943 PMCID: PMC11261685 DOI: 10.1136/jitc-2024-009427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2024] [Indexed: 07/23/2024] Open
Abstract
Therapies targeting the programmed cell death protein-1/programmed death-ligand 1 (PD-L1) (abbreviated as PD-(L)1) axis are a significant advancement in the treatment of many tumor types. However, many patients receiving these agents fail to respond or have an initial response followed by cancer progression. For these patients, while subsequent immunotherapies that either target a different axis of immune biology or non-immune combination therapies are reasonable treatment options, the lack of predictive biomarkers to follow-on agents is impeding progress in the field. This review summarizes the current knowledge of mechanisms driving resistance to PD-(L)1 therapies, the state of biomarker development along this axis, and inherent challenges in future biomarker development for these immunotherapies. Innovation in the development and application of novel biomarkers and patient selection strategies for PD-(L)1 agents is required to accelerate the delivery of effective treatments to the patients most likely to respond.
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Affiliation(s)
- Anne Monette
- Lady Davis Institute for Medical Research, Montreal, Québec, Canada
| | | | | | | | | | - Janis M Taube
- The Mark Foundation Center for Advanced Genomics and Imaging at Johns Hopkins University, Baltimore, Maryland, USA
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Valenti A, Falcone I, Valenti F, Ricciardi E, Di Martino S, Maccallini MT, Cerro M, Desiderio F, Miseo L, Russillo M, Guerrisi A. Biobanks as an Indispensable Tool in the "Era" of Precision Medicine: Key Role in the Management of Complex Diseases, Such as Melanoma. J Pers Med 2024; 14:731. [PMID: 39063985 PMCID: PMC11278009 DOI: 10.3390/jpm14070731] [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: 06/08/2024] [Revised: 07/02/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024] Open
Abstract
In recent years, medicine has undergone profound changes, strongly entering a new phase defined as the "era of precision medicine". In this context, patient clinical management involves various scientific approaches that allow for a comprehensive pathology evaluation: from preventive processes (where applicable) to genetic and diagnostic studies. In this scenario, biobanks play an important role and, over the years, have gained increasing prestige, moving from small deposits to large collections of samples of various natures. Disease-oriented biobanks are rapidly developing as they provide useful information for the management of complex diseases, such as melanoma. Indeed, melanoma, given its highly heterogeneous characteristics, is one of the oncologic diseases with the greatest clinical and therapeutic management complexity. So, the possibility of extrapolating tissue, genetic and imaging data from dedicated biobanks could result in more selective study approaches. In this review, we specifically analyze the several biobank types to evaluate their role in technology development, patient monitoring and research of new biomarkers, especially in the melanoma context.
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Affiliation(s)
- Alessandro Valenti
- Radiology and Diagnostic Imaging Unit, Department of Clinical and Dermatological Research, San Gallicano Dermatological Institute IRCCS, 00144 Rome, Italy; (F.D.); (L.M.); (A.G.)
| | - Italia Falcone
- SAFU, Department of Research, Advanced Diagnostics, and Technological Innovation, IRCCS-Regina Elena National Cancer Institute, 00144 Rome, Italy;
| | - Fabio Valenti
- UOC Oncological Translational Research, IRCCS-Regina Elena National Cancer Institute, 00144 Rome, Italy; (F.V.); (E.R.)
| | - Elena Ricciardi
- UOC Oncological Translational Research, IRCCS-Regina Elena National Cancer Institute, 00144 Rome, Italy; (F.V.); (E.R.)
| | - Simona Di Martino
- UOC Pathology Unit, Biobank IRCCS-Regina Elena National Cancer Institute, 00144 Rome, Italy;
| | - Maria Teresa Maccallini
- Department of Clinical and Molecular Medicine, Università La Sapienza di Roma, 00185 Rome, Italy; (M.T.M.); (M.C.)
| | - Marianna Cerro
- Department of Clinical and Molecular Medicine, Università La Sapienza di Roma, 00185 Rome, Italy; (M.T.M.); (M.C.)
| | - Flora Desiderio
- Radiology and Diagnostic Imaging Unit, Department of Clinical and Dermatological Research, San Gallicano Dermatological Institute IRCCS, 00144 Rome, Italy; (F.D.); (L.M.); (A.G.)
| | - Ludovica Miseo
- Radiology and Diagnostic Imaging Unit, Department of Clinical and Dermatological Research, San Gallicano Dermatological Institute IRCCS, 00144 Rome, Italy; (F.D.); (L.M.); (A.G.)
| | - Michelangelo Russillo
- Division of Medical Oncology, IRCCS-Regina Elena National Cancer Institute, 00144 Rome, Italy;
| | - Antonino Guerrisi
- Radiology and Diagnostic Imaging Unit, Department of Clinical and Dermatological Research, San Gallicano Dermatological Institute IRCCS, 00144 Rome, Italy; (F.D.); (L.M.); (A.G.)
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Cippitani R, Mandarano M, Pelliccia C, Colcelli V, Sidoni A. Biobanking-related bioethical and legal unresolved issues. Virchows Arch 2024; 485:159-160. [PMID: 36383246 DOI: 10.1007/s00428-022-03450-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 10/28/2022] [Accepted: 11/04/2022] [Indexed: 11/18/2022]
Affiliation(s)
- Roberto Cippitani
- Department of Law, University of Perugia, Perugia, Italy
- INDEPAC-Instituto Nacional de Estudios Superiores en Derecho Penal, Mexico City, Mexico
- Institute IFAC, National Research Council (Italy), Florence, Italy
| | - Martina Mandarano
- Department of Medicine and Surgery, Section of Anatomic Pathology and Histology, Medical School, University of Perugia, P.Za Lucio Severi 1, 06132, Perugia, Italy
| | - Cristina Pelliccia
- Department of Medicine and Surgery, Section of Anatomic Pathology and Histology, Medical School, University of Perugia, P.Za Lucio Severi 1, 06132, Perugia, Italy
| | | | - Angelo Sidoni
- Department of Medicine and Surgery, Section of Anatomic Pathology and Histology, Medical School, University of Perugia, P.Za Lucio Severi 1, 06132, Perugia, Italy.
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Sánchez-López AM, Catalina P, Franco F, Panadero-Fajardo S, Rejón JD, Romero-Sánchez MC, Puerta-Puerta JM, Aguilar-Quesada R. Data Model for the Comprehensive Management of Biobanks and Its Contribution to Personalized Medicine. J Pers Med 2024; 14:668. [PMID: 39063922 PMCID: PMC11277733 DOI: 10.3390/jpm14070668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/05/2024] [Accepted: 06/18/2024] [Indexed: 07/28/2024] Open
Abstract
Biobanks are infrastructures essential for research involving multi-disciplinary teams and an increasing number of stakeholders. In the field of personalized medicine, biobanks play a key role through the provision of well-characterized and annotated samples protecting at the same time the right of donors. The Andalusian Public Health System Biobank (SSPA Biobank) has implemented a global information management system made up of different modules that allow for the recording, traceability and monitoring of all the information associated with the biobank operations. The data model, designed in a standardized and normalized way according to international initiatives on data harmonization, integrates the information necessary to guarantee the quality of results from research, benefiting researchers, clinicians and donors.
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Affiliation(s)
- Ana María Sánchez-López
- Andalusian Public Health System Biobank, Coordinating Node, 18016 Granada, Spain; (P.C.); (F.F.); (S.P.-F.); (J.D.R.); (M.C.R.-S.); (J.M.P.-P.); (R.A.-Q.)
- Instituto de Investigación Biosanitaria Ibs.GRANADA, 18012 Granada, Spain
| | - Purificación Catalina
- Andalusian Public Health System Biobank, Coordinating Node, 18016 Granada, Spain; (P.C.); (F.F.); (S.P.-F.); (J.D.R.); (M.C.R.-S.); (J.M.P.-P.); (R.A.-Q.)
| | - Fernando Franco
- Andalusian Public Health System Biobank, Coordinating Node, 18016 Granada, Spain; (P.C.); (F.F.); (S.P.-F.); (J.D.R.); (M.C.R.-S.); (J.M.P.-P.); (R.A.-Q.)
| | - Sonia Panadero-Fajardo
- Andalusian Public Health System Biobank, Coordinating Node, 18016 Granada, Spain; (P.C.); (F.F.); (S.P.-F.); (J.D.R.); (M.C.R.-S.); (J.M.P.-P.); (R.A.-Q.)
| | - Juan David Rejón
- Andalusian Public Health System Biobank, Coordinating Node, 18016 Granada, Spain; (P.C.); (F.F.); (S.P.-F.); (J.D.R.); (M.C.R.-S.); (J.M.P.-P.); (R.A.-Q.)
| | - María Concepción Romero-Sánchez
- Andalusian Public Health System Biobank, Coordinating Node, 18016 Granada, Spain; (P.C.); (F.F.); (S.P.-F.); (J.D.R.); (M.C.R.-S.); (J.M.P.-P.); (R.A.-Q.)
| | - Jose Manuel Puerta-Puerta
- Andalusian Public Health System Biobank, Coordinating Node, 18016 Granada, Spain; (P.C.); (F.F.); (S.P.-F.); (J.D.R.); (M.C.R.-S.); (J.M.P.-P.); (R.A.-Q.)
- Unidad de Gestión Clínica Hematología y Hemoterapia, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain
| | - Rocío Aguilar-Quesada
- Andalusian Public Health System Biobank, Coordinating Node, 18016 Granada, Spain; (P.C.); (F.F.); (S.P.-F.); (J.D.R.); (M.C.R.-S.); (J.M.P.-P.); (R.A.-Q.)
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Domaradzki J, Czekajewska J, Walkowiak D. Trust and Support for Cancer Research Biobanks: Insights from Cancer Patients in Poland. Med Sci Monit 2024; 30:e944263. [PMID: 38867418 PMCID: PMC11184987 DOI: 10.12659/msm.944263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 03/27/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Biobanks are legally regulated entities that acquire, store, prepare, preserve, test, analyze, and distribute defined biological material and related information and data from human sources. This study aimed to evaluate trust, support and willingness to donate personal data and tissue samples for biobanking from cancer patients attending oncology departments in Poznań, Poland. MATERIAL AND METHODS This study utilized data from questionnaire-based survey conducted from February to June 2023 among 548 patients from 2 Poznań hospitals equipped with oncology treatment units. The survey employed convenience sampling. Statistical analysis was carried out using JASP 0.18.3 and PQStat1.8.6., with significance levels set at 0.05. Descriptive statistics and logistic regression were utilized to present the results. RESULTS 92.2% of cancer patients supported the establishment of cancer research biobank in Poland, and 93.1% declared the willingness to share their cancer tissues for research purposes. Patients' willingness to donate was associated with biomedical research conducted by biobanks and types of biobank institutions. Most patients were willing to donate for research on cancer, genetic and autoimmune diseases or dementia, but were reluctant to participate in research on sexual identity, intelligence, aggression and for-profit research. Patients were willing to donate to biobanks managed by medical universities, public institutions, clinical hospitals and national biobanks but not to foreign and private biobanks. CONCLUSIONS Although patients' support for cancer biobank is high it is not unconditional as their willingness to participate in cancer-related research is associated with types of biomedical research conducted by biobanks and different types of biobank institutions.
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Affiliation(s)
- Jan Domaradzki
- Department of Social Sciences and Humanities, Poznań University of Medical Sciences, Poznań, Poland
| | - Justyna Czekajewska
- Department of Social Sciences and Humanities, Poznań University of Medical Sciences, Poznań, Poland
| | - Dariusz Walkowiak
- Department of Organization and Management in Health Care, Poznań University of Medical Sciences, Poznań, Poland
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Reyes-Pérez P, Hernández-Ledesma AL, Román-López TV, García-Vilchis B, Ramírez-González D, Lázaro-Figueroa A, Martinez D, Flores-Ocampo V, Espinosa-Méndez IM, Tinajero-Nieto L, Peña-Ayala A, Morelos-Figaredo E, Guerra-Galicia CM, Torres-Valdez E, Gordillo-Huerta MV, Gandarilla-Martínez NA, Salinas-Barboza K, Félix-Rodríguez G, Frontana-Vázquez G, Matuk-Pérez Y, Estrada-Bellmann I, Alpizar-Rodríguez D, Rodríguez-Violante M, Rentería ME, Ruíz-Contreras AE, Alcauter S, Medina-Rivera A. Building national patient registries in Mexico: insights from the MexOMICS Consortium. Front Digit Health 2024; 6:1344103. [PMID: 38895515 PMCID: PMC11183280 DOI: 10.3389/fdgth.2024.1344103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 05/01/2024] [Indexed: 06/21/2024] Open
Abstract
Objective To introduce MexOMICS, a Mexican Consortium focused on establishing electronic databases to collect, cross-reference, and share health-related and omics data on the Mexican population. Methods Since 2019, the MexOMICS Consortium has established three electronic-based registries: the Mexican Twin Registry (TwinsMX), Mexican Lupus Registry (LupusRGMX), and the Mexican Parkinson's Research Network (MEX-PD), designed and implemented using the Research Electronic Data Capture web-based application. Participants were enrolled through voluntary participation and on-site engagement with medical specialists. We also acquired DNA samples and Magnetic Resonance Imaging scans in subsets of participants. Results The registries have successfully enrolled a large number of participants from a variety of regions within Mexico: TwinsMX (n = 2,915), LupusRGMX (n = 1,761) and MEX-PD (n = 750). In addition to sociodemographic, psychosocial, and clinical data, MexOMICS has collected DNA samples to study the genetic biomarkers across the three registries. Cognitive function has been assessed with the Montreal Cognitive Assessment in a subset of 376 MEX-PD participants. Furthermore, a subset of 267 twins have participated in cognitive evaluations with the Creyos platform and in MRI sessions acquiring structural, functional, and spectroscopy brain imaging; comparable evaluations are planned for LupusRGMX and MEX-PD. Conclusions The MexOMICS registries offer a valuable repository of information concerning the potential interplay of genetic and environmental factors in health conditions among the Mexican population.
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Affiliation(s)
- Paula Reyes-Pérez
- Laboratorio Internacional de Investigación Sobre el Genoma Humano, Universidad Nacional Autónoma de México, Santiago de Querétaro, Mexico
| | - Ana Laura Hernández-Ledesma
- Laboratorio Internacional de Investigación Sobre el Genoma Humano, Universidad Nacional Autónoma de México, Santiago de Querétaro, Mexico
| | - Talía V. Román-López
- Departamento de Neurobiología Conductual y Cognitiva, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Santiago de Querétaro, Mexico
| | - Brisa García-Vilchis
- Laboratorio de Neurogenómica Cognitiva, Unidad de Investigación de Psicobiología y Neurociencias, Coordinación de Psicobiología y Neurociencias, Facultad de Psicología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Diego Ramírez-González
- Departamento de Neurobiología Conductual y Cognitiva, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Santiago de Querétaro, Mexico
| | - Alejandra Lázaro-Figueroa
- Laboratorio de Neurogenómica Cognitiva, Unidad de Investigación de Psicobiología y Neurociencias, Coordinación de Psicobiología y Neurociencias, Facultad de Psicología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Domingo Martinez
- Laboratorio Internacional de Investigación Sobre el Genoma Humano, Universidad Nacional Autónoma de México, Santiago de Querétaro, Mexico
- Unidad de Genómica Avanzada, Langebio, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Mexico
- Escuela Nacional de Estudios Superiores, Unidad Juriquilla, Universidad Nacional Autónoma de México, Santiago de Querétaro, Mexico
| | - Victor Flores-Ocampo
- Laboratorio Internacional de Investigación Sobre el Genoma Humano, Universidad Nacional Autónoma de México, Santiago de Querétaro, Mexico
| | - Ian M. Espinosa-Méndez
- Departamento de Neurobiología Conductual y Cognitiva, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Santiago de Querétaro, Mexico
| | - Lizbet Tinajero-Nieto
- Hospital General Regional No. 1, Instituto Mexicano del Seguro Social, Querétaro, Santiago de Querétaro, Mexico
| | - Angélica Peña-Ayala
- Hospital General Regional No. 1, Instituto Mexicano del Seguro Social, Querétaro, Santiago de Querétaro, Mexico
- Instituto Nacional de Rehabilitación “Luis Guillermo Ibarra Ibarra”, Ciudad de México, Mexico
| | - Eugenia Morelos-Figaredo
- Hospital Regional, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Morelia, Mexico
| | | | | | - María Vanessa Gordillo-Huerta
- Hospital General Querétaro, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Santiago de Querétaro, Mexico
| | | | | | | | | | - Yamil Matuk-Pérez
- Facultad de Medicina, Universidad Autónoma de Querétaro. Unidad de Neurociencias, Hospital Angeles Centro Sur, Santiago de Querétaro, Mexico
| | - Ingrid Estrada-Bellmann
- Movement Disorders Clinic, Neurology Division, Internal Medicine Department, University Hospital “Dr. José E. González”, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | | | - Mayela Rodríguez-Violante
- Laboratorio Clínico de Enfermedades Neurodegenerativas, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, Mexico City, Mexico
| | - Miguel E. Rentería
- Mental Health and Neuroscience Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Alejandra E. Ruíz-Contreras
- Laboratorio de Neurogenómica Cognitiva, Unidad de Investigación de Psicobiología y Neurociencias, Coordinación de Psicobiología y Neurociencias, Facultad de Psicología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Sarael Alcauter
- Departamento de Neurobiología Conductual y Cognitiva, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Santiago de Querétaro, Mexico
| | - Alejandra Medina-Rivera
- Laboratorio Internacional de Investigación Sobre el Genoma Humano, Universidad Nacional Autónoma de México, Santiago de Querétaro, Mexico
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11
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Rivera-Alcántara JA, Esparza-Hurtado N, Galán-Ramírez GA, Cruz-Bautista I, Mehta R, Aguilar-Salinas CA, Martagon AJ. A systematic review of biobanks in Latin America: Strengths and limitations for biomedical research. Int J Biol Markers 2024; 39:91-106. [PMID: 38613331 DOI: 10.1177/03936155241239672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
Biobanks are valuable tools for developing and applying scientific research and international cooperation through the collection of biological materials and their associated data. Systematic research following the Preferred Reporting Items for Systematic Review and Meta-Analysis guidelines was conducted in late 2022 in PubMed and Scopus, and generated 17 articles to be reviewed in depth and critically assessed using the Critical Appraisal Skills Programme Checklist due to the limited available data; 12 relevant health organizations and government websites outside of peer-reviewed journals were also included. Our research identified 44 biobanks in Latin America. In general, there is a lack of regulation and legislation guaranteeing the stored materials' quality and institutional collaboration. We believe a consensus needs to be reached regarding the terminology and definitions used for biobanks. The design for informed consent should also be agreed upon to ensure the privacy of the data shared among institutions. In conclusion, in Latin America, there is a clear need for government support in creating specific procedures for biobanks and providing further support for existing biobanks.
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Affiliation(s)
| | | | - Gabriela A Galán-Ramírez
- Escuela de Medicina y Ciencias de la Salud, Tecnologico de Monterrey, Mexico City, Mexico
- Unidad de Investigación de Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Ivette Cruz-Bautista
- Unidad de Investigación de Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Roopa Mehta
- Unidad de Investigación de Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Carlos A Aguilar-Salinas
- Escuela de Medicina y Ciencias de la Salud, Tecnologico de Monterrey, Mexico City, Mexico
- Unidad de Investigación de Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Alexandro J Martagon
- Escuela de Medicina y Ciencias de la Salud, Tecnologico de Monterrey, Mexico City, Mexico
- Unidad de Investigación de Enfermedades Metabólicas, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- The Institute for Obesity Research, Tecnologico de Monterrey, Monterrey, Mexico
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12
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Spielau C, Bunzel C, Abert S, Baldauf H, Schmidt AH, Schetelig J. The Collaborative Biobank (CoBi): Donor and recipient samples & data to facilitate future research on hematopoietic cell transplantation. Best Pract Res Clin Haematol 2024; 37:101551. [PMID: 39098795 DOI: 10.1016/j.beha.2024.101551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/05/2024] [Accepted: 03/26/2024] [Indexed: 08/06/2024]
Abstract
Biobanking provides benefit for future generations by facilitating medical research and subsequent translation and application of research findings. Long-term storage and research involving biological material and associated data necessitate the proper implementation of ethical and legal standards. A key principle includes recognizing informed consent as a crucial element for legitimizing the collection of biological material and data. Furthermore, any collected material and data must be employed exclusively for the research framework that aligns with the explicit consent provided by the participants. Last but not least, data privacy and security are essential in biobanking. This review elucidates chances and limitations of biobanking in the field of allogeneic hematopoietic cell transplantation. We discuss the practical implementation of the requirements, illustrated by the Collaborative Biobank, a collaborative research platform for research in blood cancer.
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Affiliation(s)
| | | | - Stefan Abert
- DKMS Group gGmbH, Clinical Trials Unit, Dresden, Germany
| | | | - Alexander H Schmidt
- DKMS Group gGmbH, Clinical Trials Unit, Dresden, Germany; DKMS Group gGmbH, Tübingen, Germany
| | - Johannes Schetelig
- DKMS Group gGmbH, Clinical Trials Unit, Dresden, Germany; University Hospital Dresden, Dresden, Germany
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13
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Alebouyeh M, Almasian Tehrani N, Fallah F, Azimi L, Sadredinamin M, Yousefi N, Ghandchi G, Haji Molla Hoseini M. Protective effects of different lyoprotectants on survival of clinical bacterial isolates in a hospital biobank. Cryobiology 2024; 115:104891. [PMID: 38522663 DOI: 10.1016/j.cryobiol.2024.104891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/04/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024]
Abstract
Nowadays the significant role of biobanks in medical, diagnostic, industrial, and environmental research is well known. Bacterial biobanks could be used as a good resource for designing new treatments, biomedical and industrial researches, and laboratory diagnostics. To have a collection of bacteria from clinical samples and maintain their long-term viability, their preservation needs appropriate protective agents, like cryoprotectants and lyoprotectants. In this study, we collected and characterized Gram-negative and Gram-positive bacteria carrying important antibiotic resistance markers from different clinical samples of hospitalized children. Sucrose (10%), skimmed milk (10%), skimmed milk plus sodium glutamate (10% + 1%), and bovine serum albumin (BSA, 10%) were used as lyoprotectants during the freeze-drying procedure. The survival rate of the lyophilized samples was calculated by dilution plating and measuring the colony forming unit (CFU) after 3 months of storage. The culture analysis results indicated that 25 of the 27 studied bacterial genera (Dilutions 10-3 to 10-6), including Shigella, Methicillin-resistant S. aureus, Acinetobacter spp., Escherichia spp., Pseudomonas spp., Klebsiella spp., Enterococcus spp., were recovered in cultured fractions from all preservation conditions, while 2 genera were only detected in a single preservation condition (2/27, 7.4%). Based on the results, sucrose (10%) and skimmed milk (10%) presented the most protective features. The survival rates varied significantly according to types of the bacteria. Collectively, our results showed a diversity in the recovery of different bacterial genera after lyophilization. While statistically no significant difference was detected among the studied protective agents, sucrose (10%) and skimmed milk (10%) exhibited more effective lyoprotective properties for both Gram-positive and Gram-negative bacteria among the clinical isolates in our study.
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Affiliation(s)
- Masoud Alebouyeh
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nasim Almasian Tehrani
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Fallah
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Medical Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Leila Azimi
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehrzad Sadredinamin
- Department of Medical Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Neda Yousefi
- Department of Medical Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ghazale Ghandchi
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mostafa Haji Molla Hoseini
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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14
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Demircan Çeker D, Baysungur V, Evman S, Kolbaş İ, Gördebil A, Nalbantoğlu SM, Tambağ Y, Kaçar Ö, Midi A, Aslanoğlu H, Kara N, Algan N, Boyacioğlu A, Karademir Yilmaz B, Şahin A, Ülbeği Polat H, Şehitoğullari A, Çibikdiken AO, Büyükyilmaz M, Aydilek İB, Eneş A, Küçüker S, Karakaya F, Boyaci İ, Gümüş M, Şenol O, Öztuğ M, Saban E, Soysal Ö, Büyükpinarbaşili N, Turna A, Günlüoğlu MZ, Çakir A, Tekin Ş, Tazebay U, Karadağ A. LUNGBANK: a novel biorepository strategy tailored for comprehensive multiomics analysis and P-medicine applications in lung cancer. Turk J Biol 2024; 48:203-217. [PMID: 39050710 PMCID: PMC11265891 DOI: 10.55730/1300-0152.2696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 06/26/2024] [Accepted: 05/28/2024] [Indexed: 07/27/2024] Open
Abstract
Background/aim LUNGBANK was established as part of Project LUNGMARK, pioneering a biorepository dedicated exclusively to lung cancer research. It employs cutting-edge technologies to streamline the handling of biospecimens, ensuring the acquisition of high-quality samples. This infrastructure is fortified with robust data management capabilities, enabling seamless integration of diverse datasets. LUNGBANK functions not merely as a repository but as a sophisticated platform crucial for advancing lung cancer research, poised to facilitate significant discoveries. Materials and methods LUNGBANK was meticulously designed to optimize every stage of biospecimen handling, from collection and storage to processing. Rigorous standard operating procedures and stringent quality control measures guarantee the integrity of collected biospecimens. Advanced data management protocols facilitate the efficient integration and analysis of various datasets, enhancing the depth and breadth of research possibilities in lung cancer. Results LUNGBANK has amassed a comprehensive collection of biospecimens essential for unraveling the intricate molecular mechanisms of lung cancer. The integration of state-of-the-art technologies ensures the acquisition of top-tier data, fostering breakthroughs in translational and histological research. Moreover, the establishment of patient-derived systems by LUNGBANK underscores its pivotal role in personalized medicine approaches. Conclusion The establishment of LUNGBANK marks a significant milestone in addressing the critical challenges of lung cancer research. By providing researchers with high-quality biospecimens and advanced research tools, LUNGBANK not only supports Project LUNGMARK's objectives but also contributes extensively to the broader landscape of personalized medicine. It promises to enhance our understanding of lung cancer initiation, progression, and therapeutic interventions tailored to individual patient needs, thereby advancing the field towards more effective diagnostic and therapeutic strategies.
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Affiliation(s)
- Dilek Demircan Çeker
- Molecular Oncology Laboratory, Medical Biotechnology Research Group, VPLS, TÜBİTAK Marmara Research Center, Kocaeli, Turkiye
- Department of Molecular Biology and Genetics, Gebze Technical University, Kocaeli, Turkiye
| | - Volkan Baysungur
- Department of Thoracic Surgery, Faculty of Medicine, University of Health Sciences, İstanbul, Turkiye
- Department of Thoracic Surgery, Süreyyapaşa Training and Research Hospital, İstanbul, Turkiye
| | - Serdar Evman
- Department of Thoracic Surgery, Süreyyapaşa Training and Research Hospital, İstanbul, Turkiye
| | - İlker Kolbaş
- Department of Thoracic Surgery, Süreyyapaşa Training and Research Hospital, İstanbul, Turkiye
| | - Abdurrahim Gördebil
- Department of Thoracic Surgery, Süreyyapaşa Training and Research Hospital, İstanbul, Turkiye
| | - Sinem M Nalbantoğlu
- Molecular Oncology Laboratory, Medical Biotechnology Research Group, VPLS, TÜBİTAK Marmara Research Center, Kocaeli, Turkiye
| | - Yusuf Tambağ
- Software Technologies Research Institute, TÜBİTAK Informatics and Information Security Research Center, Ankara, Turkiye
| | - Ömer Kaçar
- Molecular Oncology Laboratory, Medical Biotechnology Research Group, VPLS, TÜBİTAK Marmara Research Center, Kocaeli, Turkiye
| | - Ahmet Midi
- Department of Pathology, Faculty of Medicine, Bahçeşehir University, İstanbul, Turkiye
| | - Hatice Aslanoğlu
- Department of Thoracic Surgery, Süreyyapaşa Training and Research Hospital, İstanbul, Turkiye
| | - Nülüfer Kara
- Department of Thoracic Surgery, Süreyyapaşa Training and Research Hospital, İstanbul, Turkiye
| | - Nilgün Algan
- Department of Thoracic Surgery, Süreyyapaşa Training and Research Hospital, İstanbul, Turkiye
| | - Ayberk Boyacioğlu
- Department of Thoracic Surgery, Süreyyapaşa Training and Research Hospital, İstanbul, Turkiye
| | - Betül Karademir Yilmaz
- Division of Biochemistry, Department of Basic Medical Sciences, Faculty of Medicine, Marmara University, İstanbul, Turkiye
- Genetic and Metabolic Diseases Research and Investigation Center (GEMHAM), Marmara University, İstanbul, Turkiye
| | - Ali Şahin
- Division of Biochemistry, Department of Basic Medical Sciences, Faculty of Medicine, Marmara University, İstanbul, Turkiye
- Genetic and Metabolic Diseases Research and Investigation Center (GEMHAM), Marmara University, İstanbul, Turkiye
| | - Hivda Ülbeği Polat
- Molecular Oncology Laboratory, Medical Biotechnology Research Group, VPLS, TÜBİTAK Marmara Research Center, Kocaeli, Turkiye
| | - Abidin Şehitoğullari
- Department of Thoracic Surgery, Faculty of Medicine, Sakarya University, Sakarya, Turkiye
| | - Ali Osman Çibikdiken
- Department of Computer Sciences and Engineering, KTO Karatay University, Konya, Turkiye
| | | | - İbrahim Berkan Aydilek
- Department of Computer Engineering, Faculty of Engineering, Harran University, Şanlıurfa, Turkiye
| | - Abdulkerim Eneş
- Department of Computer Engineering, Faculty of Engineering, Harran University, Şanlıurfa, Turkiye
| | - Sevde Küçüker
- Molecular Oncology Laboratory, Medical Biotechnology Research Group, VPLS, TÜBİTAK Marmara Research Center, Kocaeli, Turkiye
| | - Fatih Karakaya
- Molecular Oncology Laboratory, Medical Biotechnology Research Group, VPLS, TÜBİTAK Marmara Research Center, Kocaeli, Turkiye
| | - İhsan Boyaci
- Department of Internal Medicine, Faculty of Medicine, İstanbul Medipol University, İstanbul, Turkiye
| | - Mahmut Gümüş
- Department of Internal Medicine, Faculty of Medicine, İstanbul Medeniyet University, İstanbul, Turkiye
| | - Onur Şenol
- Department of Analytical Chemistry, Faculty of Pharmacy, Atatürk University, Erzurum, Turkiye
| | - Merve Öztuğ
- TÜBİTAK National Metrology Institute, Kocaeli, Turkiye
| | - Evren Saban
- TÜBİTAK National Metrology Institute, Kocaeli, Turkiye
| | - Ömer Soysal
- Department of Thoracic Surgery, Faculty of Medicine, Bezmialem Vakıf University, İstanbul, Turkiye
| | - Nur Büyükpinarbaşili
- Department of Pathology, Faculty of Medicine, Bezmialem Vakıf University, İstanbul, Turkiye
| | - Akif Turna
- Department of Thoracic Surgery, Faculty of Medicine, İstanbul University-Cerrahpaşa, İstanbul, Turkiye
| | - Mehmet Zeki Günlüoğlu
- Department of Thoracic Surgery, Faculty of Medicine, İstanbul Medipol University, İstanbul, Turkiye
| | - Aslı Çakir
- Department of Pathology, Faculty of Medicine, İstanbul Medipol University, İstanbul, Turkiye
| | - Şaban Tekin
- Division of Medical Biology, Department of Basic Medical Sciences, Faculty of Medicine, University of Health Sciences, İstanbul, Turkiye
| | - Uygar Tazebay
- Department of Molecular Biology and Genetics, Gebze Technical University, Kocaeli, Turkiye
| | - Abdullah Karadağ
- Molecular Oncology Laboratory, Medical Biotechnology Research Group, VPLS, TÜBİTAK Marmara Research Center, Kocaeli, Turkiye
- Institute of Biotechnology, Gebze Technical University, Kocaeli, Turkiye
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15
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Masucci M, Karlsson C, Blomqvist L, Ernberg I. Bridging the Divide: A Review on the Implementation of Personalized Cancer Medicine. J Pers Med 2024; 14:561. [PMID: 38929782 PMCID: PMC11204735 DOI: 10.3390/jpm14060561] [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: 04/11/2024] [Revised: 05/05/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
The shift towards personalized cancer medicine (PCM) represents a significant transformation in cancer care, emphasizing tailored treatments based on the genetic understanding of cancer at the cellular level. This review draws on recent literature to explore key factors influencing PCM implementation, highlighting the role of innovative leadership, interdisciplinary collaboration, and coordinated funding and regulatory strategies. Success in PCM relies on overcoming challenges such as integrating diverse medical disciplines, securing sustainable investment for shared infrastructures, and navigating complex regulatory landscapes. Effective leadership is crucial for fostering a culture of innovation and teamwork, essential for translating complex biological insights into personalized treatment strategies. The transition to PCM necessitates not only organizational adaptation but also the development of new professional roles and training programs, underscoring the need for a multidisciplinary approach and the importance of team science in overcoming the limitations of traditional medical paradigms. The conclusion underscores that PCM's success hinges on creating collaborative environments that support innovation, adaptability, and shared vision among all stakeholders involved in cancer care.
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Affiliation(s)
- Michele Masucci
- Department of Learning, Informatics, Management and Ethics (LIME), Karolinska Institutet, Tomtebodavägen 18B, 171 65 Solna, Sweden
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden
| | - Claes Karlsson
- Department of Oncology-Pathology (Onc-Pat), Karolinska Institutet, Anna Steckséns gata 30A, D2:04, 171 65 Solna, Sweden;
| | - Lennart Blomqvist
- Department of Molecular Medicine and Surgery (MMK), Karolinska Institutet, Anna Steckséns gata 53, 171 65 Solna, Sweden;
| | - Ingemar Ernberg
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Solnavägen 9, 171 65 Solna, Sweden
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16
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Domaradzki J, Majchrowska A, Cielecka-Piontek J, Walkowiak D. Do biobanks need pharmacists? Support of pharmacy students to biobanking of human biological material for pharmaceutical research and development. Front Pharmacol 2024; 15:1406866. [PMID: 38799162 PMCID: PMC11117077 DOI: 10.3389/fphar.2024.1406866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 04/23/2024] [Indexed: 05/29/2024] Open
Abstract
Objectives This study aimed to assess the biobank awareness among Polish pharmacy students and how it affects their support for biobank research. Methods A survey among 366 pharmacy students enrolled at two Polish medical universities: the Poznań University of Medical Sciences and Medical University of Lublin was conducted. Results Although most pharmacy students felt positivity about biobanking and expressed the willingness to donate their biospecimens for biomedical research, their awareness on research biobanks was low. Their willingness to participate was driven by the desire to benefit society, help advance science and develop new therapies. While students supported donation for most types of research, biobanks run by medical universities were the highest trusted research institutions. The primary factors associated with student's willingness to participate were religiosity and place of study. Notably, nonreligious students and those studying in Poznan exhibited more favourable attitudes toward donating for research and expressed greater support for the establishment of research biobanks in Poland. Conclusion Since biobank awareness among future pharmacists is inadequate incorporating biobank competency domains into education and training of pharmacists is required.
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Affiliation(s)
- Jan Domaradzki
- Department of Social Sciences and Humanities, Poznan University of Medical Sciences, Poznań, Poland
| | - Anita Majchrowska
- Chair and Department of Humanities and Social Medicine, Medical University of Lublin, Lublin, Poland
| | - Judyta Cielecka-Piontek
- Department of Pharmacognosy and Biomaterials, Poznan University of Medical Sciences, Poznań, Poland
| | - Dariusz Walkowiak
- Department of Organization and Management in Healthcare, Poznan University of Medical Sciences, Poznań, Poland
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17
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Næss M, Kvaløy K, Sørgjerd EP, Sætermo KS, Norøy L, Røstad AH, Hammer N, Altø TG, Vikdal AJ, Hveem K. Data Resource Profile: The HUNT Biobank. Int J Epidemiol 2024; 53:dyae073. [PMID: 38836303 PMCID: PMC11150882 DOI: 10.1093/ije/dyae073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 05/23/2024] [Indexed: 06/06/2024] Open
Affiliation(s)
- Marit Næss
- HUNT Research Centre, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - Kirsti Kvaløy
- HUNT Research Centre, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
- Department of Community Medicine, Center for Sami Health Research, Arctic University of Norway, Tromso, Norway
| | - Elin P Sørgjerd
- HUNT Research Centre, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - Kristin S Sætermo
- HUNT Research Centre, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - Lise Norøy
- HUNT Research Centre, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - Ann Helen Røstad
- HUNT Research Centre, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - Nina Hammer
- HUNT Research Centre, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - Trine Govasli Altø
- HUNT Research Centre, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - Anne Jorunn Vikdal
- HUNT Research Centre, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - Kristian Hveem
- HUNT Research Centre, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Center for Molecular and Clinical Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology), Trondheim, Norway
- Department of Research, St Olav’s Hospital, Trondheim, Norway
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18
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Youssef O, Loukola A, Zidi-Mouaffak YHS, Tamlander M, Ruotsalainen S, Kilpeläinen E, Mars N, Ripatti S, Palotie A, Donner K, Carpén O. High-Resolution Genotyping of Formalin-Fixed Tissue Accurately Estimates Polygenic Risk Scores in Human Diseases. J Transl Med 2024; 104:100325. [PMID: 38220043 DOI: 10.1016/j.labinv.2024.100325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 12/11/2023] [Accepted: 01/05/2024] [Indexed: 01/16/2024] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues stored in biobanks and pathology archives are a vast but underutilized source for molecular studies on different diseases. Beyond being the "gold standard" for preservation of diagnostic human tissues, FFPE samples retain similar genetic information as matching blood samples, which could make FFPE samples an ideal resource for genomic analysis. However, research on this resource has been hindered by the perception that DNA extracted from FFPE samples is of poor quality. Here, we show that germline disease-predisposing variants and polygenic risk scores (PRS) can be identified from FFPE normal tissue (FFPE-NT) DNA with high accuracy. We optimized the performance of FFPE-NT DNA on a genome-wide array containing 657,675 variants. Via a series of testing and validation phases, we established a protocol for FFPE-NT genotyping with results comparable with blood genotyping. The median call rate of FFPE-NT samples in the validation phase was 99.85% (range 98.26%-99.94%) and median concordance with matching blood samples was 99.79% (range 98.85%-99.9%). We also demonstrated that a rare pathogenic PALB2 genetic variant predisposing to cancer can be correctly identified in FFPE-NT samples. We further imputed the FFPE-NT genotype data and calculated the FFPE-NT genome-wide PRS in 3 diseases and 4 disease risk variables. In all cases, FFPE-NT and matching blood PRS were highly concordant (all Pearson's r > 0.95). The ability to precisely genotype FFPE-NT on a genome-wide array enables translational genomics applications of archived FFPE-NT samples with the possibility to link to corresponding phenotypes and longitudinal health data.
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Affiliation(s)
- Omar Youssef
- Department of Pathology, University of Helsinki, Helsinki, Finland; Clinical and Chemical Pathology Department, National Cancer Institute, Cairo University, Cairo, Egypt; Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
| | - Anu Loukola
- Helsinki Biobank, Helsinki University Hospital (HUS), Helsinki, Finland
| | - Yossra H S Zidi-Mouaffak
- Department of Pathology, University of Helsinki, Helsinki, Finland; Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Helsinki Biobank, Helsinki University Hospital (HUS), Helsinki, Finland
| | - Max Tamlander
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Sanni Ruotsalainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Elina Kilpeläinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Nina Mars
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland; Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland; Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Clinicum, Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland; Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Psychiatric and Neurodevelopmental Genetics Unit, Department of Psychiatry, Analytic and Translational Genetics Unit, Department of Medicine, and the Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts
| | - Kati Donner
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Olli Carpén
- Department of Pathology, University of Helsinki, Helsinki, Finland; Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Helsinki Biobank, Helsinki University Hospital (HUS), Helsinki, Finland
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Walkowiak D, Miraleyeva A, Batyrova T, Domaradzki J. Support for Research Biobanks Among Medical Students in the Republic of Kazakhstan. Biopreserv Biobank 2024. [PMID: 38527285 DOI: 10.1089/bio.2023.0114] [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: 03/27/2024] Open
Abstract
Background: Over the past few years, several biobanks have been organized in the Republic of Kazakhstan (RoK). As research biobanks are becoming an increasingly important tool for precision medicine, they require competent biobankers who will help disseminate the idea of biobanking throughout the society and support donation for research purposes. This study aimed to assess the support for research biobanks among medical students (MSs) in Kazakhstan. Methods: This research includes data from an anonymous, self-administered online questionnaire regarding MSs' support for research biobanks in the RoK. Results: Only 212 (31.3%) MSs have heard of biobanks and 466 (68.7%) have not. Students who were biobank-aware held more positive views regarding biobanks, were more likely to support the idea of establishing a research biobank in Kazakhstan, and expressed a greater willingness to donate their biological material for research purposes. Students' awareness of biobanks was also associated with the respondents' motivations to donate. Students who were familiar with biobanks tended to be motivated by altruistic reasons more often, and those unfamiliar with biobanks tended to indicate selfish motives. Students' attitudes toward donation to various types of research and biobanks were influenced by their awareness of biobanks, any family history of genetic disease, experience of chronic disease, declared religiousness, hospitalization history, blood donor status, and year of study. Conclusion: Since MSs' awareness of research biobanks is low, there is an urgent need for biobank education in Kazakhstan.
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Affiliation(s)
- Dariusz Walkowiak
- Department of Organization and Management in Health Care, Poznan University of Medical Sciences, Poznań, Poland
| | - Alua Miraleyeva
- Department of Psychology, West Kazakhstan Marat Ospanov Medical University, Aktobe, Kazakhstan
| | - Tamara Batyrova
- Department of Normal Physiology, West Kazakhstan Marat Ospanov Medical University, Aktobe, Kazakhstan
| | - Jan Domaradzki
- Department of Social Sciences and Humanities, Poznan University of Medical Sciences, Poznań, Poland
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20
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Eccher A, Seminati D, L’Imperio V, Casati G, Pilla D, Malapelle U, Piga I, Bindi G, Marando A, Bonoldi E, Dainese E, Riefolo M, D’Errico A, Costantini M, Lugli A, Grassi S, Scarpa A, Dei Tos AP, Pagni F. Pathology Laboratory Archives: Conservation Quality of Nucleic Acids and Proteins for NSCLC Molecular Testing. J Pers Med 2024; 14:333. [PMID: 38672960 PMCID: PMC11050929 DOI: 10.3390/jpm14040333] [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: 02/22/2024] [Revised: 03/15/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024] Open
Abstract
In the molecular era, proper archival conditions within pathology laboratories are crucial, especially for formalin-fixed paraffin-embedded (FFPE) tissue specimens retrieved years after the original diagnosis. Indeed, improper preservation can impact the integrity of nucleic acids and protein antigens. This study evaluates the quality status of stored FFPE blocks using multilevel omics approaches. FFPE blocks from 45 Non-Small Cell Lung Carcinoma (NSCLC) cases were analyzed. The blocks were collected from six different pathology archives across Italy with distinct environmental characteristics. Nucleic acids' quantity and quality, as well as protein antigens, were assessed using various techniques, including MALDI-MSI. RNA was quantitatively higher, but more fragmented, compared to DNA. DNA quantity and quality were suitable for molecular analyses in 94.4% and 62.3% of samples, respectively. RNA quantity was adequate across all samples, but it was optimal only in 22.3% of cases. DNA quality started to deteriorate after 6-8 years, whereas RNA quality diminished only after 10 years of storage. These data might suggest a particular DNA susceptibility to FFPE blocks conservation. Immunohistochemical intensity decreased significantly after 6-8 years of storage, and MALDI-MSI analysis revealed that younger tissue blocks contained more unique proteomic signals than the older ones. This study emphasizes the importance of proper FFPE archiving conditions for molecular analyses. Governance should prioritize attention to pathology archives to ensure quality preservation and optimize predictive testing. By elucidating the nuances of FFPE block storage, this research paves the way for enhanced molecular diagnostics and therapeutic insights regarding oncology and beyond.
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Affiliation(s)
- Albino Eccher
- Department of Diagnostics and Public Health, University of Modena and Reggio Emilia, 41121 Modena, Italy;
| | - Davide Seminati
- Department of Medicine and Surgery, Pathology, Fondazione IRCCS San Gerardo dei Tintori, University of Milano-Bicocca, 20900 Monza, Italy; (V.L.); (G.C.); (D.P.); (F.P.)
| | - Vincenzo L’Imperio
- Department of Medicine and Surgery, Pathology, Fondazione IRCCS San Gerardo dei Tintori, University of Milano-Bicocca, 20900 Monza, Italy; (V.L.); (G.C.); (D.P.); (F.P.)
| | - Gabriele Casati
- Department of Medicine and Surgery, Pathology, Fondazione IRCCS San Gerardo dei Tintori, University of Milano-Bicocca, 20900 Monza, Italy; (V.L.); (G.C.); (D.P.); (F.P.)
| | - Daniela Pilla
- Department of Medicine and Surgery, Pathology, Fondazione IRCCS San Gerardo dei Tintori, University of Milano-Bicocca, 20900 Monza, Italy; (V.L.); (G.C.); (D.P.); (F.P.)
| | - Umberto Malapelle
- Department of Public Health, Pathology, University of Naples Federico II, 80131 Naples, Italy;
| | - Isabella Piga
- Department of Biomedical Sciences, University of Cagliari, 09124 Cagliari, Italy;
- Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy;
| | - Greta Bindi
- Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy;
| | - Alessandro Marando
- Department of Pathology, ASST Grande Ospedale Niguarda, 20162 Milan, Italy; (A.M.); (E.B.)
| | - Emanuela Bonoldi
- Department of Pathology, ASST Grande Ospedale Niguarda, 20162 Milan, Italy; (A.M.); (E.B.)
| | - Emanuele Dainese
- Department of Pathology, ASST Valtellina e Alto Lario, 23100 Sondrio, Italy;
| | - Mattia Riefolo
- Pathology Unit, Department of Diagnostic Medicine and Prevention, Sant’Orsola-Malpighi Hospital, University of Bologna, 40138 Bologna, Italy; (M.R.); (A.D.)
| | - Antonia D’Errico
- Pathology Unit, Department of Diagnostic Medicine and Prevention, Sant’Orsola-Malpighi Hospital, University of Bologna, 40138 Bologna, Italy; (M.R.); (A.D.)
| | - Matteo Costantini
- Department of Pathology, University Hospital of Modena, 41121 Modena, Italy; (M.C.); (A.L.)
| | - Alberto Lugli
- Department of Pathology, University Hospital of Modena, 41121 Modena, Italy; (M.C.); (A.L.)
| | - Stefano Grassi
- Pathology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy;
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37126 Verona, Italy;
| | - Angelo Paolo Dei Tos
- Department of Pathology, University of Padua School of Medicine, Azienda Ospedale Università Padova, 35122 Padua, Italy;
| | - Fabio Pagni
- Department of Medicine and Surgery, Pathology, Fondazione IRCCS San Gerardo dei Tintori, University of Milano-Bicocca, 20900 Monza, Italy; (V.L.); (G.C.); (D.P.); (F.P.)
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21
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Faysal H, Quinney SK, Haas DM. Facilitating global collaborations for pregnancy and pediatric biomarker research through a biobank database: the Collaborative Online Perinatal & Pediatric Repository project. Am J Obstet Gynecol MFM 2024; 6:101304. [PMID: 38286324 PMCID: PMC11165967 DOI: 10.1016/j.ajogmf.2024.101304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 01/31/2024]
Affiliation(s)
- Hani Faysal
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, 550 N University Blvd., UH 2440, Indianapolis, IN 46202.
| | - Sara K Quinney
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN; Maternal and Pediatric Precision in Therapeutics (MPRINT) Hub, Indiana University School of Medicine, Indianapolis, IN
| | - David M Haas
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN
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22
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Aurora L, Wanderley MRB. Signaling Pathways in Hypertrophic Cardiomyopathy: Will Proteomic Profiling Guide the Future? J Card Fail 2024; 30:473-475. [PMID: 37890654 DOI: 10.1016/j.cardfail.2023.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023]
Affiliation(s)
- Lindsey Aurora
- Henry Ford Heart and Vascular Institute, Henry Ford Health, Detroit, MI.
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23
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Ferreira B, Barros AS, Leite-Pereira C, Viegas J, das Neves J, Nunes R, Sarmento B. Trends in 3D models of inflammatory bowel disease. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167042. [PMID: 38296115 DOI: 10.1016/j.bbadis.2024.167042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/11/2023] [Accepted: 01/25/2024] [Indexed: 02/20/2024]
Abstract
Inflammatory bowel disease (IBD) encompasses a set of chronic inflammatory conditions, namely Crohn's disease and ulcerative colitis. Despite all advances in the management of IBD, a definitive cure is not available, largely due to a lack of a holistic understanding of its etiology and pathophysiology. Several in vitro, in vivo, and ex vivo models have been developed over the past few decades in order to abbreviate remaining gaps. The establishment of reliable and predictable in vitro intestinal inflammation models may indeed provide valuable tools to expedite and validate the development of therapies for IBD. Three-dimensional (3D) models provide a more accurate representation of the different layers of the intestine, contributing to a stronger impact on drug screening and research on intestinal inflammation, and bridging the gap between in vitro and in vivo research. This work provides a critical overview on the state-of-the-art on existing 3D models of intestinal inflammation and discusses the remaining challenges, providing insights on possible pathways towards achieving IBD mimetic models. We also address some of the main challenges faced by implementing cell culture models in IBD research while bearing in mind clinical translational aspects.
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Affiliation(s)
- Bárbara Ferreira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Andreia S Barros
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Catarina Leite-Pereira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Juliana Viegas
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - José das Neves
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; IUCS-CESPU - Instituto Universitário de Ciências da Saúde, Rua Central de Gandra 1317, 4585-116 Gandra, Portugal
| | - Rute Nunes
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; IUCS-CESPU - Instituto Universitário de Ciências da Saúde, Rua Central de Gandra 1317, 4585-116 Gandra, Portugal
| | - Bruno Sarmento
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; INEB - Instituto de Engenharia Biomédica, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; IUCS-CESPU - Instituto Universitário de Ciências da Saúde, Rua Central de Gandra 1317, 4585-116 Gandra, Portugal.
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24
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Brancato V, Esposito G, Coppola L, Cavaliere C, Mirabelli P, Scapicchio C, Borgheresi R, Neri E, Salvatore M, Aiello M. Standardizing digital biobanks: integrating imaging, genomic, and clinical data for precision medicine. J Transl Med 2024; 22:136. [PMID: 38317237 PMCID: PMC10845786 DOI: 10.1186/s12967-024-04891-8] [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: 11/28/2023] [Accepted: 01/14/2024] [Indexed: 02/07/2024] Open
Abstract
Advancements in data acquisition and computational methods are generating a large amount of heterogeneous biomedical data from diagnostic domains such as clinical imaging, pathology, and next-generation sequencing (NGS), which help characterize individual differences in patients. However, this information needs to be available and suitable to promote and support scientific research and technological development, supporting the effective adoption of the precision medicine approach in clinical practice. Digital biobanks can catalyze this process, facilitating the sharing of curated and standardized imaging data, clinical, pathological and molecular data, crucial to enable the development of a comprehensive and personalized data-driven diagnostic approach in disease management and fostering the development of computational predictive models. This work aims to frame this perspective, first by evaluating the state of standardization of individual diagnostic domains and then by identifying challenges and proposing a possible solution towards an integrative approach that can guarantee the suitability of information that can be shared through a digital biobank. Our analysis of the state of the art shows the presence and use of reference standards in biobanks and, generally, digital repositories for each specific domain. Despite this, standardization to guarantee the integration and reproducibility of the numerical descriptors generated by each domain, e.g. radiomic, pathomic and -omic features, is still an open challenge. Based on specific use cases and scenarios, an integration model, based on the JSON format, is proposed that can help address this problem. Ultimately, this work shows how, with specific standardization and promotion efforts, the digital biobank model can become an enabling technology for the comprehensive study of diseases and the effective development of data-driven technologies at the service of precision medicine.
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Affiliation(s)
| | - Giuseppina Esposito
- Bio Check Up S.R.L, 80121, Naples, Italy
- Department of Advanced Biomedical Sciences, University of Naples Federico II, 80131, Naples, Italy
| | | | | | - Peppino Mirabelli
- UOS Laboratori di Ricerca e Biobanca, AORN Santobono-Pausilipon, Via Teresa Ravaschieri, 8, 80122, Naples, Italy
| | - Camilla Scapicchio
- Academic Radiology, Department of Translational Research, University of Pisa, via Roma, 67, 56126, Pisa, Italy
| | - Rita Borgheresi
- Academic Radiology, Department of Translational Research, University of Pisa, via Roma, 67, 56126, Pisa, Italy
| | - Emanuele Neri
- Academic Radiology, Department of Translational Research, University of Pisa, via Roma, 67, 56126, Pisa, Italy
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25
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Yu L, Shen XJ, Liu H, Zhou YT, Zhang Q, Zhang ZD, Shen SM. Effect of ultrasound-guided continuous erector spinae plane block on postoperative pain and inflammatory response in patients undergoing modified radical mastectomy for breast cancer: study protocol for a randomised controlled trial. Trials 2024; 25:51. [PMID: 38225606 PMCID: PMC10788999 DOI: 10.1186/s13063-023-07777-0] [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: 04/21/2023] [Accepted: 11/06/2023] [Indexed: 01/17/2024] Open
Abstract
BACKGROUND A single injection of local anaesthetic (LA) in the erector spinae plane block (ESPB) can reduce pain after modified radical mastectomy (MRM) surgery, but the duration of analgesia is affected by the duration of the LA. The aim of this study is to investigate the effect of continuous ESPB on acute and chronic pain and inflammatory response after MRM surgery. METHODS In this prospective, randomised, controlled trial, we will recruit 160 patients, aged 18-80 years, scheduled for elective MRM surgery under general anaesthesia. They will be randomly assigned to two groups: a continuous ESPB group (group E) and a sham block group (group C). Both groups of patients will have a nerve block (group C pretended to puncture) and an indwelling catheter fixed prior to surgery. Electronic pumps containing LA are shielded. The primary outcome is the total consumption of analgesic agents. The secondary outcomes include the levels of inflammation-related cytokines; the occurrence of chronic pain (post-mastectomy pain syndrome, PMPS); static and dynamic pain scores at 2, 6, 12, 24 and 48 h postoperatively; and post-operative and post-puncture adverse reactions. DISCUSSION Analgesia after MRM surgery is important and chronic pain can develop when acute pain is prolonged, but the analgesic effect of a nerve block with a single injection of LA is limited by the duration of drug action. The aim of this trial is to investigate whether continuous ESPB can reduce acute pain after MRM surgery and reduce the incidence of chronic pain (PMPS), with fewer postoperative analgesic drug-related complications and less inflammatory response. Continuous ESPB and up to 12 months of follow-up are two innovations of this trial. TRIAL REGISTRATION Chinese Clinical Trial Registry ( https://www.chictr.org.cn/ ) ChiCTR2200061935. Registered on 11 July 2022. This trial is a prospective registry with the following registry names: Effect of ultrasound-guided continuous erector spinae plane block on postoperative pain and inflammatory response in patients undergoing modified radical mastectomy for breast cancer.
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Affiliation(s)
- Liang Yu
- Department of Anesthesiology, Huzhou Central Hospital, The Fifth School of Clinical Medicine of Zhejiang Chinese Medical University, The Affiliated Huzhou Hospital, Zhejiang University School of Medicine, Affiliated Central Hospital, Huzhou University, No. 1558 Sanhuan North Road, Huzhou, 313000, Zhejiang, China
| | - Xiao-Juan Shen
- Department of 706A Ward Nursing, Huzhou Central Hospital, The Fifth School of Clinical Medicine of Zhejiang Chinese Medical University, The Affiliated Huzhou Hospital, Zhejiang University School of Medicine, Affiliated Central Hospital, Huzhou University, No. 1558 Sanhuan North Road, Huzhou, 313000, Zhejiang, China.
| | - He Liu
- Department of Anesthesiology, Huzhou Central Hospital, The Fifth School of Clinical Medicine of Zhejiang Chinese Medical University, The Affiliated Huzhou Hospital, Zhejiang University School of Medicine, Affiliated Central Hospital, Huzhou University, No. 1558 Sanhuan North Road, Huzhou, 313000, Zhejiang, China
| | - Yu-Ting Zhou
- Department of Breast Surgery, Huzhou Central Hospital, The Fifth School of Clinical Medicine of Zhejiang Chinese Medical University, The Affiliated Huzhou Hospital, Zhejiang University School of Medicine, Affiliated Central Hospital, Huzhou University, No. 1558 Sanhuan North Road, Huzhou, 313000, Zhejiang, China
| | - Qin Zhang
- Department of Anesthesiology, Huzhou Central Hospital, The Fifth School of Clinical Medicine of Zhejiang Chinese Medical University, The Affiliated Huzhou Hospital, Zhejiang University School of Medicine, Affiliated Central Hospital, Huzhou University, No. 1558 Sanhuan North Road, Huzhou, 313000, Zhejiang, China
| | - Zhen-Duo Zhang
- Department of Anesthesiology, Huzhou Central Hospital, The Fifth School of Clinical Medicine of Zhejiang Chinese Medical University, The Affiliated Huzhou Hospital, Zhejiang University School of Medicine, Affiliated Central Hospital, Huzhou University, No. 1558 Sanhuan North Road, Huzhou, 313000, Zhejiang, China
| | - Shu-Min Shen
- Department of Anesthesiology, Huzhou Central Hospital, The Fifth School of Clinical Medicine of Zhejiang Chinese Medical University, The Affiliated Huzhou Hospital, Zhejiang University School of Medicine, Affiliated Central Hospital, Huzhou University, No. 1558 Sanhuan North Road, Huzhou, 313000, Zhejiang, China
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26
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Tio ES, Misztal MC, Felsky D. Evidence for the biopsychosocial model of suicide: a review of whole person modeling studies using machine learning. Front Psychiatry 2024; 14:1294666. [PMID: 38274429 PMCID: PMC10808719 DOI: 10.3389/fpsyt.2023.1294666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024] Open
Abstract
Background Traditional approaches to modeling suicide-related thoughts and behaviors focus on few data types from often-siloed disciplines. While psychosocial aspects of risk for these phenotypes are frequently studied, there is a lack of research assessing their impact in the context of biological factors, which are important in determining an individual's fulsome risk profile. To directly test this biopsychosocial model of suicide and identify the relative importance of predictive measures when considered together, a transdisciplinary, multivariate approach is needed. Here, we systematically review the emerging literature on large-scale studies using machine learning to integrate measures of psychological, social, and biological factors simultaneously in the study of suicide. Methods We conducted a systematic review of studies that used machine learning to model suicide-related outcomes in human populations including at least one predictor from each of biological, psychological, and sociological data domains. Electronic databases MEDLINE, EMBASE, PsychINFO, PubMed, and Web of Science were searched for reports published between August 2013 and August 30, 2023. We evaluated populations studied, features emerging most consistently as risk or resilience factors, methods used, and strength of evidence for or against the biopsychosocial model of suicide. Results Out of 518 full-text articles screened, we identified a total of 20 studies meeting our inclusion criteria, including eight studies conducted in general population samples and 12 in clinical populations. Common important features identified included depressive and anxious symptoms, comorbid psychiatric disorders, social behaviors, lifestyle factors such as exercise, alcohol intake, smoking exposure, and marital and vocational status, and biological factors such as hypothalamic-pituitary-thyroid axis activity markers, sleep-related measures, and selected genetic markers. A minority of studies conducted iterative modeling testing each data type for contribution to model performance, instead of reporting basic measures of relative feature importance. Conclusion Studies combining biopsychosocial measures to predict suicide-related phenotypes are beginning to proliferate. This literature provides some early empirical evidence for the biopsychosocial model of suicide, though it is marred by harmonization challenges. For future studies, more specific definitions of suicide-related outcomes, inclusion of a greater breadth of biological data, and more diversity in study populations will be needed.
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Affiliation(s)
- Earvin S. Tio
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Melissa C. Misztal
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Daniel Felsky
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
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27
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Chowdhury MA, Zhang JJ, Rizk R, Chen WCW. Stem cell therapy for heart failure in the clinics: new perspectives in the era of precision medicine and artificial intelligence. Front Physiol 2024; 14:1344885. [PMID: 38264333 PMCID: PMC10803627 DOI: 10.3389/fphys.2023.1344885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 12/26/2023] [Indexed: 01/25/2024] Open
Abstract
Stem/progenitor cells have been widely evaluated as a promising therapeutic option for heart failure (HF). Numerous clinical trials with stem/progenitor cell-based therapy (SCT) for HF have demonstrated encouraging results, but not without limitations or discrepancies. Recent technological advancements in multiomics, bioinformatics, precision medicine, artificial intelligence (AI), and machine learning (ML) provide new approaches and insights for stem cell research and therapeutic development. Integration of these new technologies into stem/progenitor cell therapy for HF may help address: 1) the technical challenges to obtain reliable and high-quality therapeutic precursor cells, 2) the discrepancies between preclinical and clinical studies, and 3) the personalized selection of optimal therapeutic cell types/populations for individual patients in the context of precision medicine. This review summarizes the current status of SCT for HF in clinics and provides new perspectives on the development of computation-aided SCT in the era of precision medicine and AI/ML.
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Affiliation(s)
- Mohammed A. Chowdhury
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD, United States
- Department of Public Health and Health Sciences, Health Sciences Ph.D. Program, School of Health Sciences, University of South Dakota, Vermillion, SD, United States
- Department of Cardiology, North Central Heart, Avera Heart Hospital, Sioux Falls, SD, United States
| | - Jing J. Zhang
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD, United States
| | - Rodrigue Rizk
- Department of Computer Science, University of South Dakota, Vermillion, SD, United States
| | - William C. W. Chen
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD, United States
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28
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Berrino E, Bellomo SE, Chesta A, Detillo P, Bragoni A, Gagliardi A, Naccarati A, Cereda M, Witel G, Sapino A, Bussolati B, Bussolati G, Marchiò C. Alternative Tissue Fixation Protocols Dramatically Reduce the Impact of DNA Artifacts, Unraveling the Interpretation of Clinical Comprehensive Genomic Profiling. J Transl Med 2024; 104:100280. [PMID: 38345263 DOI: 10.1016/j.labinv.2023.100280] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 10/03/2023] [Accepted: 10/25/2023] [Indexed: 02/15/2024] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) samples represent the cornerstone of tissue-based analysis in precision medicine. Targeted next-generation sequencing panels are routinely used to analyze a limited number of genes to guide treatment decision-making for advanced-stage patients. The number and complexity of genetic alterations to be investigated are rapidly growing; in several instances, a comprehensive genomic profiling analysis is needed. The poor quality of genetic material extracted from FFPE samples may impact the feasibility/reliability of sequencing data. We sampled 9 colorectal cancers to allow 4 parallel fixations: (1) neutral buffered formalin (NBF), (2) acid-deprived formalin fixation (ADF), (3) precooled ADF (coldADF), and (4) glyoxal acid free (GAF). DNA extraction, fragmentation analysis, and sequencing by 2 large next-generation sequencing panels (OCAv3 and TSO500) followed. We comprehensively analyzed library and sequencing quality controls and the quality of sequencing results. Libraries from coldADF samples showed significantly longer reads than the others with both panels. ADF-derived and coldADF-derived libraries showed the lowest level of noise and the highest levels of uniformity with the OCAv3 panel, followed by GAF and NBF samples. The data uniformity was confirmed by the TSO500 results, which also highlighted the best performance in terms of the total region sequenced for the ADF and coldADF samples. NBF samples had a significantly smaller region sequenced and displayed a significantly lower number of evaluable microsatellite loci and a significant increase in single-nucleotide variations compared with other protocols. Mutational signature 1 (aging and FFPE artifact related) showed the highest (37%) and lowest (17%) values in the NBF and coldADF samples, respectively. Most of the identified genetic alterations were shared by all samples in each lesion. Five genes showed a different mutational status across samples and/or panels: 4 discordant results involved NBF samples. In conclusion, acid-deprived fixatives (GAF and ADF) guarantee the highest DNA preservation/sequencing performance, thus allowing more complex molecular profiling of tissue samples.
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Affiliation(s)
- Enrico Berrino
- Department of Medical Sciences, University of Turin, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy.
| | | | - Anita Chesta
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy
| | | | - Alberto Bragoni
- Department of Medical Sciences, University of Turin, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy
| | - Amedeo Gagliardi
- Department of Medical Sciences, University of Turin, Turin, Italy; IIGM-Italian Institute for Genomic Medicine, c/o IRCCS, Candiolo, TO, Italy
| | - Alessio Naccarati
- Department of Medical Sciences, University of Turin, Turin, Italy; IIGM-Italian Institute for Genomic Medicine, c/o IRCCS, Candiolo, TO, Italy
| | - Matteo Cereda
- IIGM-Italian Institute for Genomic Medicine, c/o IRCCS, Candiolo, TO, Italy
| | - Gianluca Witel
- Department of Medical Sciences, University of Turin, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy
| | - Anna Sapino
- Department of Medical Sciences, University of Turin, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy
| | - Benedetta Bussolati
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Gianni Bussolati
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Caterina Marchiò
- Department of Medical Sciences, University of Turin, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy.
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Rassomakhina NV, Ryazanova AY, Likhov AR, Bruskin SA, Maloshenok LG, Zherdeva VV. Tumor Organoids: The Era of Personalized Medicine. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:S127-S147. [PMID: 38621748 DOI: 10.1134/s0006297924140086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/01/2023] [Accepted: 11/09/2023] [Indexed: 04/17/2024]
Abstract
The strategies of future medicine are aimed to modernize and integrate quality approaches including early molecular-genetic profiling, identification of new therapeutic targets and adapting design for clinical trials, personalized drug screening (PDS) to help predict and individualize patient treatment regimens. In the past decade, organoid models have emerged as an innovative in vitro platform with the potential to realize the concept of patient-centered medicine. Organoids are spatially restricted three-dimensional clusters of cells ex vivo that self-organize into complex functional structures through genetically programmed determination, which is crucial for reconstructing the architecture of the primary tissue and organs. Currently, there are several strategies to create three-dimensional (3D) tumor systems using (i) surgically resected patient tissue (PDTOs, patient-derived tumor organoids) or (ii) single tumor cells circulating in the patient's blood. Successful application of 3D tumor models obtained by co-culturing autologous tumor organoids (PDTOs) and peripheral blood lymphocytes have been demonstrated in a number of studies. Such models simulate a 3D tumor architecture in vivo and contain all cell types characteristic of this tissue, including immune system cells and stem cells. Components of the tumor microenvironment, such as fibroblasts and immune system cells, affect tumor growth and its drug resistance. In this review, we analyzed the evolution of tumor models from two-dimensional (2D) cell cultures and laboratory animals to 3D tissue-specific tumor organoids, their significance in identifying mechanisms of antitumor response and drug resistance, and use of these models in drug screening and development of precision methods in cancer treatment.
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Affiliation(s)
- Natalia V Rassomakhina
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Alexandra Yu Ryazanova
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Astemir R Likhov
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Sergey A Bruskin
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Liliya G Maloshenok
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Victoria V Zherdeva
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia.
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30
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Tavares NT, Lobo J, Bagrodia A. MicroRNAs for detecting occult genitourinary cancer. Curr Opin Urol 2024; 34:20-26. [PMID: 37916954 DOI: 10.1097/mou.0000000000001137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
PURPOSE OF REVIEW Genitourinary (GU) malignancies are a real burden in global health worldwide. Each model has its own clinical challenges, and the early screening and/or detection of occult cancer in follow-up is transversal to all of them. MicroRNAs (miRNAs) have been proposed as minimally invasive liquid biopsy cancer biomarkers, due to their stability and low degradation. RECENT FINDINGS The different GU tumor models are in different stages concerning miRNAs as biomarkers for cancer detection. Testicular germ cell tumors (TGCTs) already have a specific defined target, miR-371a-3p, that has shown high sensitivity and specificity in different clinical settings, and is now in final stages of preanalytical testing before entering the clinic. The other GU malignancies are in a different stage, with many liquid biopsy studies (both in urine and plasma/serum) being currently performed, but there is not an agreeable miRNA or set of miRNAs that is ready to follow the footsteps of miR-371a-3p in TGCTs. SUMMARY Further studies with proper molecular characterization of miRNA profiles of GU malignancies and standardization of sampling, biobanking and formal analysis may aid in the advance and choosing of specific target sets to be used for occult cancer detection.
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Affiliation(s)
- Nuno Tiago Tavares
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre Raquel Seruca (Porto.CCC)
- Doctoral Programme in Biomedical Sciences, School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP)
| | - João Lobo
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre Raquel Seruca (Porto.CCC)
- Department of Pathology, Portuguese Oncology Institute of Porto/Porto Comprehensive Cancer Centre Raquel Seruca (Porto.CCC)
- Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
| | - Aditya Bagrodia
- Department of Urology, University of California - San Diego Health, San Diego, California
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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31
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Kamenskikh EM, Krygina AY, Gomboeva SC, Zhailebaeva D, Koval DP, Kicherov NA, Otchurzhap CN, Birulina YG, Alifirova VM. [Biobanking in clinical trials involving multiple sclerosis patients]. Zh Nevrol Psikhiatr Im S S Korsakova 2024; 124:7-15. [PMID: 39175234 DOI: 10.17116/jnevro20241240727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
Investigation of multiple sclerosis (MS) pathogenesis requires sophisticated analytical tools of precision medicine, such as omics research, which include genomics, microbiomics and metabolomics (proteomics, lipidomics and glycomics). Such sensitive methods are based on careful preanalytical work with biomaterials to maintain quality and obtain objective results. Implementation of biobanking as a universal method for working with biomaterials will help to standardize the stages of research, compare different scientific team's results. Collaboration of MS researchers with large biobanks can also help to conduct multicenter and long-term prospective studies, to include a wide number of patients. In this article, we analyze the experience of biobanking practice technologies in studies of MS patients and share the experience of partnership between the Center for MS of the Tomsk Region and the Bank of Biological Material of the Siberian State Medical University.
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Affiliation(s)
| | - A Yu Krygina
- Siberian State Medical University, Tomsk, Russia
| | | | | | - D P Koval
- Siberian State Medical University, Tomsk, Russia
| | - N A Kicherov
- Siberian State Medical University, Tomsk, Russia
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32
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Batheja D, Goel S, Fransman W, Mantsoki A, Ongarello S, Laxminarayan R. Understanding the value of biobank attributes to researchers using a conjoint experiment. Sci Rep 2023; 13:22728. [PMID: 38123601 PMCID: PMC10733358 DOI: 10.1038/s41598-023-49394-6] [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: 05/24/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
Biobanks are important in biomedical and public health research, and future healthcare research relies on their strength and capacity. However, there are financial challenges related to the operation of commercial biobanks and concerns around the commercialization of biobanks. Non-commercial biobanks depend on grant funding to operate and could be valuable to researchers if they can enable access to quality specimens at lower costs. The objective of this study is to estimate the value of specific biobank attributes. We used a rating-based conjoint experiment approach to study how researchers valued handling fee, access, quality, characterization, breadth of consent, access to key endemics, and time taken to fulfil requests. We found that researchers placed the greatest relative importance on the quality of specimens (26%), followed by the characterization of specimens (21%). Researchers with prior experience purchasing biological samples also valued access to key endemic in-country sites (11.6%) and low handling fees (5.5%) in biobanks.
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Affiliation(s)
- Deepshikha Batheja
- One Health Trust, Obeya Pulse, First Floor, 7/1, Halasur Road, Bengaluru, Karnataka, 560102, India.
| | - Srishti Goel
- One Health Trust, Obeya Pulse, First Floor, 7/1, Halasur Road, Bengaluru, Karnataka, 560102, India
| | | | | | | | - Ramanan Laxminarayan
- One Health Trust, Obeya Pulse, First Floor, 7/1, Halasur Road, Bengaluru, Karnataka, 560102, India
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33
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du Cros P, Greig J, Alffenaar JWC, Cross GB, Cousins C, Berry C, Khan U, Phillips PPJ, Velásquez GE, Furin J, Spigelman M, Denholm JT, Thi SS, Tiberi S, Huang GKL, Marks GB, Turkova A, Guglielmetti L, Chew KL, Nguyen HT, Ong CWM, Brigden G, Singh KP, Motta I, Lange C, Seddon JA, Nyang'wa BT, Maug AKJ, Gler MT, Dooley KE, Quelapio M, Tsogt B, Menzies D, Cox V, Upton CM, Skrahina A, McKenna L, Horsburgh CR, Dheda K, Marais BJ. Standards for clinical trials for treating TB. Int J Tuberc Lung Dis 2023; 27:885-898. [PMID: 38042969 PMCID: PMC10719894 DOI: 10.5588/ijtld.23.0341] [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: 07/25/2023] [Accepted: 08/21/2023] [Indexed: 12/04/2023] Open
Abstract
BACKGROUND: The value, speed of completion and robustness of the evidence generated by TB treatment trials could be improved by implementing standards for best practice.METHODS: A global panel of experts participated in a Delphi process, using a 7-point Likert scale to score and revise draft standards until consensus was reached.RESULTS: Eleven standards were defined: Standard 1, high quality data on TB regimens are essential to inform clinical and programmatic management; Standard 2, the research questions addressed by TB trials should be relevant to affected communities, who should be included in all trial stages; Standard 3, trials should make every effort to be as inclusive as possible; Standard 4, the most efficient trial designs should be considered to improve the evidence base as quickly and cost effectively as possible, without compromising quality; Standard 5, trial governance should be in line with accepted good clinical practice; Standard 6, trials should investigate and report strategies that promote optimal engagement in care; Standard 7, where possible, TB trials should include pharmacokinetic and pharmacodynamic components; Standard 8, outcomes should include frequency of disease recurrence and post-treatment sequelae; Standard 9, TB trials should aim to harmonise key outcomes and data structures across studies; Standard 10, TB trials should include biobanking; Standard 11, treatment trials should invest in capacity strengthening of local trial and TB programme staff.CONCLUSION: These standards should improve the efficiency and effectiveness of evidence generation, as well as the translation of research into policy and practice.
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Affiliation(s)
- P du Cros
- Burnet Institute, Melbourne, VIC, Monash Infectious Diseases, Monash Health, Melbourne, VIC, Australia
| | - J Greig
- Burnet Institute, Melbourne, VIC, Médecins Sans Frontières (MSF), Manson Unit, London, UK
| | - J-W C Alffenaar
- Sydney Infectious Diseases Institute (Sydney ID), and, School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Westmead Hospital, Sydney, NSW
| | - G B Cross
- Burnet Institute, Melbourne, VIC, Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - C Cousins
- Department of Pharmacology and Therapeutics, University of Liverpool, Liverpool, Institute of Clinical Trials and Methodology, University College London, London, UK
| | - C Berry
- Médecins Sans Frontières (MSF), Manson Unit, London, UK
| | - U Khan
- Interactive Research and Development Global, Singapore City, Singapore
| | - P P J Phillips
- UCSF Center for Tuberculosis, Division of Pulmonary and Critical Care Medicine, and
| | - G E Velásquez
- UCSF Center for Tuberculosis, Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA
| | - J Furin
- Harvard Medical School, Department of Global Health and Social Medicine, Boston, MA
| | - M Spigelman
- Global Alliance for TB Drug Development, New York, NY, USA
| | - J T Denholm
- Victorian Tuberculosis Program, Melbourne Health, Melbourne, VIC, Department of Infectious Diseases, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - S S Thi
- Eswatini National TB Control Program, Mbabane, Kingdom of Eswatini
| | - S Tiberi
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, GlaxoSmithKline, London, UK
| | - G K L Huang
- Burnet Institute, Melbourne, VIC, Northern Health Infectious Diseases, Northern Health, Melbourne, VIC
| | - G B Marks
- School of Clinical Medicine, University of New South Wales, Sydney, NSW, Australia
| | - A Turkova
- Medical Research Council Clinical Trials Unit at University College London, London, UK
| | - L Guglielmetti
- Médecins Sans Frontières (MSF), Paris, Sorbonne Université, Institut national de la santé et de la recherche médicale, Unité 1135, Centre d'Immunologie et des Maladies Infectieuses, Paris, Assistance Publique Hôpitaux de Paris (APHP), Groupe Hospitalier Universitaire Sorbonne Université, Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries, Paris, France
| | - K L Chew
- Department of Laboratory Medicine, National University Hospital, Singapore City, Singapore
| | - H T Nguyen
- Research Department, Friends for International TB Relief, Ha Noi, Vietnam
| | - C W M Ong
- Infectious Diseases Translational Research Programme, Department of Medicine, National University of Singapore, Singapore City, Division of Infectious Diseases, Department of Medicine, National University Hospital, Singapore City, Institute of Healthcare Innovation & Technology, National University of Singapore, Singapore City, Singapore
| | - G Brigden
- The Global Fund, Geneva, Switzerland
| | - K P Singh
- Department of Infectious Diseases, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia, Victorian Infectious Disease Unit, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | | | - C Lange
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, German Center for Infection Research (DZIF), TTU-TB, Borstel, Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - J A Seddon
- Department of Infectious Disease, Imperial College London, London, UK, Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Stellenbosch University, Tygerberg, South Africa
| | - B-T Nyang'wa
- Public Health Department, Operational Center Amsterdam (OCA), MSF, Amsterdam, The Netherlands
| | - A K J Maug
- Damien Foundation Bangladesh, Dhaka, Bangladesh
| | - M T Gler
- De La Salle Medical and Health Sciences Institute, Dasmariñas, the Philippines
| | - K E Dooley
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M Quelapio
- Tropical Disease Foundation, Makati City, Manila, the Philippines, KNCV Tuberculosis Foundation, The Hague, The Netherlands
| | - B Tsogt
- Mongolian Anti-TB Coalition, Ulaanbaatar, Mongolia
| | - D Menzies
- Respiratory Epidemiology and Clinical Research Unit, Montreal Chest Institute & McGill International TB Centre, Montreal, QC, Canada
| | - V Cox
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town
| | - C M Upton
- TASK Applied Science, Cape Town, South Africa
| | - A Skrahina
- The Republican Scientific and Practical Center for Pulmonology and TB, Minsk, Belarus
| | - L McKenna
- Treatment Action Group, New York, NY
| | - C R Horsburgh
- Departments of Global Health, Epidemiology, Biostatistics and Medicine, Schools of Public Health and Medicine, Boston University, Boston MA, USA
| | - K Dheda
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa, Faculty of Infectious and Tropical Diseases, Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, UK
| | - B J Marais
- Sydney Infectious Diseases Institute (Sydney ID), and, The Children's Hospital at Westmead, Sydney, NSW, WHO Collaborating Centre in Tuberculosis, The University of Sydney, Sydney, NSW, Australia
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34
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Ezzat S, de Herder WW, Volante M, Grossman A. The Driver Role of Pathologists in Endocrine Oncology: What Clinicians Seek in Pathology Reports. Endocr Pathol 2023; 34:437-454. [PMID: 37166678 PMCID: PMC10733199 DOI: 10.1007/s12022-023-09768-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/24/2023] [Indexed: 05/12/2023]
Abstract
Endocrine neoplasia represents an increasingly broad spectrum of disorders. Endocrine neoplasms range from incidental findings to potentially lethal malignancies. In this paper, we cover the impact of pathology in the interpretation of the clinic-pathological, genetic, and radiographic features underpinning these neoplasms. We highlight the critical role of multidisciplinary interactions in structuring a rational diagnostic and efficient therapeutic plan and emphasize the role of histopathological input in decision-making. In this context, standardized pathology reporting and second opinion endocrine pathology review represent relevant tools to improve the overall diagnostic workup of patients affected by endocrine tumors in every specific scenario. In fact, although a relevant proportion of cases may be correctly identified based on clinical presentation and biochemical/imaging investigations, a subset of cases presents with atypical findings that may lead to an inappropriate diagnosis and treatment plan based on a wrong pathological diagnosis if all pieces of the puzzle are not correctly considered. Pathologists have a responsibility to actively guide clinicians before and during surgical procedures to prevent unnecessary interventions. In all areas of endocrine pathology, pathologists must understand the complexity of tissue preservation and assay sensitivities and specificities to ensure the optimal quality and interpretation of diagnostic material. Finally, pathologists are central actors in tumor tissue biobanking, which is an expanding field in oncology that should be promoted while adhering to strict ethical and methodological standards.
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Affiliation(s)
- Shereen Ezzat
- Endocrine Oncology Site Group, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Wouter W de Herder
- Department of Internal Medicine, Sector of Endocrinology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marco Volante
- Department of Oncology, University of Turin, San Luigi Hospital, Regione Gonzole 10, 10043, Orbassano, Turin, Italy.
| | - Ashley Grossman
- Barts and the London School of Medicine, University of London, London, UK
- Green Templeton College, University of Oxford, Oxford, UK
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35
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Chang Z, Hu H, Pan X, Liu C, Liu K, Zhang Y, Xu S, Cheng J, Zhang Q, Wan Q, Xiao L, Liang X, Huang H, Cheng ZJ, Sun B. Impact of ultra-low temperature storage on serum sIgE detection and allergic disease biobank feasibility. Sci Rep 2023; 13:20814. [PMID: 38012234 PMCID: PMC10682422 DOI: 10.1038/s41598-023-47915-x] [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: 10/07/2023] [Accepted: 11/20/2023] [Indexed: 11/29/2023] Open
Abstract
Research has shown that the concentration and composition of biological samples may change after long-term ultra-low temperature storage. Consequently, this study examined the effect of ultra-low temperature storage on serum sIgE detection by comparing sIgE concentrations at various durations from the time of sample storage to subsequent testing. We selected 40 serum samples from the Guangzhou Medical University Affiliated First Hospital Biobank, which had been tested for house dust mites, dog hair, tobacco mold, cockroaches, and cow milk allergen sIgE. Samples were categorized by storage duration: 14 samples stored for 10 years, 12 for 5 years, and 14 for 3 years. They were also classified by sIgE positive levels: 15 samples at levels 1-2, 15 at levels 3-4, and 10 at levels 5-6. The allergen sIgE of these samples was retested using the same technology. Regardless of the type of allergen or the level of positivity, the majority of sIgE concentrations measured at the time of storage were higher than the current measurements, but the difference was not statistically significant. The correlation between the sIgE results at the time of storage and the current results was high for samples stored for 10 years (rs = 0.991, P < 0.001) and 5 years (rs = 0.964, P < 0.001). Serum allergen sIgE is stable when stored under ultra-low temperature conditions, making the construction of a biological sample bank for allergic diseases feasible. This will facilitate researchers in quickly obtaining samples, conducting technical research, and translating findings, thereby promoting the development of the field of allergy through integration of industry, academia, and research.
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Affiliation(s)
- Zhenglin Chang
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Haisheng Hu
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaocong Pan
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Changlian Liu
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Kemin Liu
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yanxi Zhang
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shiliang Xu
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jiahao Cheng
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qitai Zhang
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qiongqiong Wan
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lexin Xiao
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xueqing Liang
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Huimin Huang
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Zhangkai J Cheng
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Baoqing Sun
- Department of Clinical Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
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36
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Sulaieva ON, Artamonova O, Dudin O, Semikov R, Urakov D, Zakharash Y, Kacharian A, Strilka V, Mykhalchuk I, Haidamak O, Serdyukova O, Kobyliak N. Ethical navigation of biobanking establishment in Ukraine: learning from the experience of developing countries. JOURNAL OF MEDICAL ETHICS 2023:jme-2023-109129. [PMID: 37945338 DOI: 10.1136/jme-2023-109129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 10/28/2023] [Indexed: 11/12/2023]
Abstract
Building a biobank network in developing countries is essential to foster genomic research and precision medicine for patients' benefit. However, there are serious barriers to establishing biobanks in low-income and middle-income countries (LMICs), including Ukraine. Here, we outline key barriers and essential milestones for the successful expansion of biobanks, genomic research and personalised medicine in Ukraine, drawing from the experience of other LMICs. A lack of legal and ethical governance in conjunction with limited awareness about biobanking and community distrust are the principal threats to establishing biobanks. The experiences of LMICs suggest that Ukraine urgently needs national guidelines covering ethical and legal aspects of biospecimen-related research. National guidelines must be consistent with international ethical recommendations for safeguarding participants' rights, welfare and privacy. Additionally, efforts to educate and engage physicians and patient communities are essential for achieving biobanking goals and benefits for precision medicine and future patients.
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Affiliation(s)
- Oksana N Sulaieva
- Department of Pathology, Medical Laboratory CSD, Kyiv, Ukraine
- Doctorate in Bioethics, Neiswanger Institute for Bioethics, Loyola University Chicago, Chicago, Illinois, USA
- Ukrainian Association of Research Biobanks, Kyiv, Ukraine
| | | | - Oleksandr Dudin
- Department of Pathology, Medical Laboratory CSD, Kyiv, Ukraine
| | - Rostyslav Semikov
- Ukrainian Association of Research Biobanks, Kyiv, Ukraine
- Audubon Bioscience, Kyiv, Ukraine
| | - Dmytro Urakov
- Ukrainian Association of Research Biobanks, Kyiv, Ukraine
| | | | | | | | - Ivan Mykhalchuk
- Ukrainian Association of Research Biobanks, Kyiv, Ukraine
- Audubon Bioscience, Kyiv, Ukraine
| | | | - Olena Serdyukova
- Ukrainian Association of Research Biobanks, Kyiv, Ukraine
- Audubon Bioscience, Kyiv, Ukraine
| | - Nazarii Kobyliak
- Department of Pathology, Medical Laboratory CSD, Kyiv, Ukraine
- Department of Endocrinology, Bogomolets National Medical University, Kyiv, Ukraine
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37
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Zheng L, Wang L. Comprehensive information management system for a medical research cohort biobank based on quality by design. BMC Med Inform Decis Mak 2023; 23:222. [PMID: 37845654 PMCID: PMC10580628 DOI: 10.1186/s12911-023-02318-w] [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: 02/13/2023] [Accepted: 09/30/2023] [Indexed: 10/18/2023] Open
Abstract
BACKGROUND With the development of big health and big data, cohort research has become a medical research hotspot. As an important repository of human genetic resources, biobanks must adapt to the requirements of large-scale and efficient operation. Thus, biobanks urgently need to design and build a legal, convenient, and efficient information management system. METHODS This study applies the concept of "quality by design" to build a comprehensive biobank information management system based on the analysis of user requirements, legal and regulatory risks, and industry-standard requirements. The system integrates the management of scientific research projects, biological specimens, clinical information, quality control, and multi-dimensional information query and development. After 10 months of its operation, the comprehensive management system was evaluated through statistical analysis of the efficiency of the construction of the pregnancy-birth cohort and the quality of genetic resources. RESULTS Since the system's launch, the statistics on cohort construction efficiency show that the enrollment rate of eligible pregnant women has increased, and the rate of missing volunteers has dropped. The time needed to establish a 1000-person cohort (with complete biological samples and clinical information in early, middle, and late pregnancy) was reduced, and the effective tracking rate of the samples was 77.42%. The error rate of the deep cryogenic refrigerator decreased, with a clinical information integrity rate of 96.47%. CONCLUSIONS The comprehensive biobank information management system constructed with the "quality by design" concept is well suited to meet the requirements of medical research. This study provides a solution for designing a comprehensive information system for medical institutions' biobanks.
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Affiliation(s)
- Lianshuai Zheng
- Biobank of Lianyungang Maternal and Child Health Hospital, Lianyungang Maternal and Child Health Hospital, Jiangsu, China
| | - Leilei Wang
- Biobank of Lianyungang Maternal and Child Health Hospital, Lianyungang Maternal and Child Health Hospital, Jiangsu, China.
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Eccher A, Dei Tos AP, Scarpa A, L'Imperio V, Munari E, Troncone G, Naccarato AG, Seminati D, Pagni F. Cost analysis of archives in the pathology laboratories: from safety to management. J Clin Pathol 2023; 76:659-663. [PMID: 37532289 PMCID: PMC10511949 DOI: 10.1136/jcp-2023-209035] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 07/26/2023] [Indexed: 08/04/2023]
Abstract
CONTEXT Despite the reluctance to invest and the challenging estimation of necessary supporting costs, optimising the archives seems to be one of the hottest topics in the future management of the pathology laboratories. Historically, archives were only partially designed to securely store and organise tissue specimens, and tracking systems were often flawed, posing significant risks to patients' health and legal ramifications for pathologists. OBJECTIVE The current review explores the available data from the literature on archives' management in pathology, including comprehensive business plans, structure setup, outfit, inventories, ongoing conservation and functional charges. DATA SOURCES Electronic searches in PubMed-MEDLINE and Embase were made to extract pertinent articles from the literature. Works about the archiving process and storage were included and analysed to extract information. Prepublication servers were ignored. Italian Institutional Regional databases for public competitive bidding processes were queried too. CONCLUSIONS A new emergent feeling in the pathology laboratory is growing for archives management; the digital pathology era is a great opportunity to apply innovation to tracking systems and samples preservation. The main aim is a critical evaluation of the return of investment in developing automatic and tracked archiving processes for improving not only quality, efficacy and efficiency of the labs but also patients' healthcare.
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Affiliation(s)
- Albino Eccher
- Department of Diagnostics and Public Health, Università degli Studi di Verona, Verona, Italy
| | | | - Aldo Scarpa
- Department of Diagnostics and Public Health, Università degli Studi di Verona, Verona, Italy
| | - Vincenzo L'Imperio
- Department of Medicine and Surgery, Pathology, University of Milan-Bicocca, Milano, Italy
| | - Enrico Munari
- Department of Pathology, University of Brescia, Brescia, Italy
| | - Giancarlo Troncone
- Public Health, University of Naples Federico II School of Medicine and Surgery, Napoli, Italy
| | | | - Davide Seminati
- Department of Medicine and Surgery, Pathology, University of Milan-Bicocca, Milano, Italy
| | - Fabio Pagni
- Department of Medicine and Surgery, Pathology, University of Milan-Bicocca, Milano, Italy
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Yang W, Ma W, Huang J, Cai Y, Peng X, Zhao F, Zhang D, Zou Z, Sun H, Qi X, Ge M. Beijing Children's Hospital guidelines on the design and conduction of the first standardized database for medulloblastoma. Metab Brain Dis 2023; 38:2393-2400. [PMID: 37261631 DOI: 10.1007/s11011-023-01233-3] [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: 03/21/2023] [Accepted: 05/09/2023] [Indexed: 06/02/2023]
Abstract
Medulloblastoma (MB) is one of the most common malignant childhood brain tumors (WHO grade IV). Its high degree of malignancy leads to an unsatisfactory prognosis, requiring more precise and personalized treatment in the near future. Multi-omics and artificial intelligence have been playing a significant role in precise medical research, but their implementation needs a large amount of clinical information and biomaterials. For these reasons, it is urgent for current MB researchers to establish a large sample-size database of MB that contains complete clinical data and sufficient biomaterials such as blood, cerebrospinal fluid (CSF), cancer tissue, and urine. Unfortunately, there are few biobanks of pediatric central nervous system (CNS) tumors throughout the world for limited specimens, scarce funds, different standards collecting methods and et cl. Even though, China falls behind western countries in this area. The present research set up a standard workflow to construct the Beijing Children's Hospital Medulloblastoma (BCH-MB) biobank. Clinical data from children with MB and for collecting and storing biomaterials, along with regular follow-up has been collected and recorded in this database. In the future, the BCH-MB biobank could make it possible to validate the promising biomarkers already identified, discover unrevealed MB biomarkers, develop novel therapies, and establish personalized prognostic models for children with MB upon the support of its sufficient data and biomaterials, laying the foundation for individualized therapies of children with MB.
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Affiliation(s)
- Wei Yang
- Department of Neurosurgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Wenping Ma
- Department of Neurosurgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Jiansong Huang
- Department of Neurosurgery, Peking University International Hospital, Peking University Health Science Center, Peking University, Beijing, 102200, China
| | - Yingjie Cai
- Department of Neurosurgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Xiaojiao Peng
- Department of Neurosurgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Fengmao Zhao
- Department of Neurosurgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Di Zhang
- Department of Neurosurgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Zhewei Zou
- Department of Neurosurgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Hailang Sun
- Department of Neurosurgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.
| | - Xiang Qi
- Department of Neurosurgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.
| | - Ming Ge
- Department of Neurosurgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.
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Geiger J, Schacter B, Coallier F. Biobanking: A Cornerstone of Biodigital Convergence. Biopreserv Biobank 2023; 21:439-441. [PMID: 37861655 DOI: 10.1089/bio.2023.29126.editorial] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023] Open
Affiliation(s)
- Jörg Geiger
- Head of Body Fluids Biobank and Biobank Laboratory University of Wuerzburg Interdisciplinary Bank for Biological Materials and Data (ibdw), Wuerzburg, Germany
| | - Brent Schacter
- CancerCare Manitoba/University of Manitoba, Winnipeg, Canada
| | - Francois Coallier
- Department of software and IT engineering, École de technologie supérieure, Montréal, Québec, Canada
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Botter SM, Kessler TM. Neuro-Urology and Biobanking: An Integrated Approach for Advancing Research and Improving Patient Care. Int J Mol Sci 2023; 24:14281. [PMID: 37762582 PMCID: PMC10531693 DOI: 10.3390/ijms241814281] [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: 08/14/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Understanding the molecular mechanisms underlying neuro-urological disorders is crucial for the development of targeted therapeutic interventions. Through the establishment of comprehensive biobanks, researchers can collect and store various biological specimens, including urine, blood, tissue, and DNA samples, to study these mechanisms. In the context of neuro-urology, biobanking facilitates the identification of genetic variations, epigenetic modifications, and gene expression patterns associated with neurogenic lower urinary tract dysfunction. These conditions often present as symptoms of neurological diseases such as Alzheimer's disease, multiple sclerosis, Parkinson's disease, spinal cord injury, and many others. Biobanking of tissue specimens from such patients is essential to understand why these diseases cause the respective symptoms and what can be done to alleviate them. The utilization of high-throughput technologies, such as next-generation sequencing and gene expression profiling, enables researchers to explore the molecular landscape of these conditions in an unprecedented manner. The development of specific and reliable biomarkers resulting from these efforts may help in early detection, accurate diagnosis, and effective monitoring of neuro-urological conditions, leading to improved patient care and management. Furthermore, these biomarkers could potentially facilitate the monitoring of novel therapies currently under investigation in neuro-urological clinical trials. This comprehensive review explores the synergistic integration of neuro-urology and biobanking, with particular emphasis on the translation of biobanking approaches in molecular research in neuro-urology. We discuss the advantages of biobanking in neuro-urological studies, the types of specimens collected and their applications in translational research. Furthermore, we highlight the importance of standardization and quality assurance when collecting samples and discuss challenges that may compromise sample quality and impose limitations on their subsequent utilization. Finally, we give recommendations for sampling in multicenter studies, examine sustainability issues associated with biobanking, and provide future directions for this dynamic field.
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Affiliation(s)
- Sander M. Botter
- Swiss Center for Musculoskeletal Biobanking, Balgrist Campus AG, 8008 Zürich, Switzerland
| | - Thomas M. Kessler
- Department of Neuro-Urology, Balgrist University Hospital, University of Zürich, 8008 Zürich, Switzerland;
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Frascarelli C, Bonizzi G, Musico CR, Mane E, Cassi C, Guerini Rocco E, Farina A, Scarpa A, Lawlor R, Reggiani Bonetti L, Caramaschi S, Eccher A, Marletta S, Fusco N. Revolutionizing Cancer Research: The Impact of Artificial Intelligence in Digital Biobanking. J Pers Med 2023; 13:1390. [PMID: 37763157 PMCID: PMC10532470 DOI: 10.3390/jpm13091390] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/05/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Biobanks are vital research infrastructures aiming to collect, process, store, and distribute biological specimens along with associated data in an organized and governed manner. Exploiting diverse datasets produced by the biobanks and the downstream research from various sources and integrating bioinformatics and "omics" data has proven instrumental in advancing research such as cancer research. Biobanks offer different types of biological samples matched with rich datasets comprising clinicopathologic information. As digital pathology and artificial intelligence (AI) have entered the precision medicine arena, biobanks are progressively transitioning from mere biorepositories to integrated computational databanks. Consequently, the application of AI and machine learning on these biobank datasets holds huge potential to profoundly impact cancer research. METHODS In this paper, we explore how AI and machine learning can respond to the digital evolution of biobanks with flexibility, solutions, and effective services. We look at the different data that ranges from specimen-related data, including digital images, patient health records and downstream genetic/genomic data and resulting "Big Data" and the analytic approaches used for analysis. RESULTS These cutting-edge technologies can address the challenges faced by translational and clinical research, enhancing their capabilities in data management, analysis, and interpretation. By leveraging AI, biobanks can unlock valuable insights from their vast repositories, enabling the identification of novel biomarkers, prediction of treatment responses, and ultimately facilitating the development of personalized cancer therapies. CONCLUSIONS The integration of biobanking with AI has the potential not only to expand the current understanding of cancer biology but also to pave the way for more precise, patient-centric healthcare strategies.
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Affiliation(s)
- Chiara Frascarelli
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy; (C.F.); (E.M.); (E.G.R.); (N.F.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Giuseppina Bonizzi
- Biobank for Translational and Digital Medicine, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy; (G.B.); (C.R.M.); (C.C.)
| | - Camilla Rosella Musico
- Biobank for Translational and Digital Medicine, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy; (G.B.); (C.R.M.); (C.C.)
| | - Eltjona Mane
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy; (C.F.); (E.M.); (E.G.R.); (N.F.)
| | - Cristina Cassi
- Biobank for Translational and Digital Medicine, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy; (G.B.); (C.R.M.); (C.C.)
| | - Elena Guerini Rocco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy; (C.F.); (E.M.); (E.G.R.); (N.F.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Annarosa Farina
- Central Information Systems and Technology Directorate, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy;
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Pathology, University of Verona, 37134 Verona, Italy; (A.S.); (S.M.)
| | - Rita Lawlor
- ARC-Net Research Centre and Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy;
| | - Luca Reggiani Bonetti
- Section of Pathology, Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, University Hospital of Modena, 41121 Modena, Italy; (L.R.B.); (S.C.)
| | - Stefania Caramaschi
- Section of Pathology, Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, University Hospital of Modena, 41121 Modena, Italy; (L.R.B.); (S.C.)
| | - Albino Eccher
- Section of Pathology, Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, University Hospital of Modena, 41121 Modena, Italy; (L.R.B.); (S.C.)
| | - Stefano Marletta
- Department of Diagnostics and Public Health, Section of Pathology, University of Verona, 37134 Verona, Italy; (A.S.); (S.M.)
- Division of Pathology, Humanitas Cancer Center, 95045 Catania, Italy
| | - Nicola Fusco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy; (C.F.); (E.M.); (E.G.R.); (N.F.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
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Assirelli E, Naldi S, Brusi V, Ciaffi J, Lisi L, Mancarella L, Pignatti F, Pulsatelli L, Faldini C, Ursini F, Neri S. Building a rheumatology biobank for reliable basic/translational research and precision medicine. Front Med (Lausanne) 2023; 10:1228874. [PMID: 37746090 PMCID: PMC10513757 DOI: 10.3389/fmed.2023.1228874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/07/2023] [Indexed: 09/26/2023] Open
Abstract
Research biobanks are non-profit structures that collect, manipulate, store, analyze and distribute systematically organized biological samples and data for research and development purposes. Over the recent years, we have established a biobank, the Rheumatology BioBank (RheumaBank) headed by the Medicine and Rheumatology unit of the IRCCS Istituto Ortopedico Rizzoli (IOR) in Bologna, Italy for the purpose of collecting, processing, storing, and distributing biological samples and associated data obtained from patients suffering from inflammatory joint diseases. RheumaBank is a research biobank, and its main objective is to promote large-scale, high-quality basic, translational, and clinical research studies that can help elucidate pathogenetic mechanisms and improve personalization of treatment choice in patients with rheumatoid arthritis (RA), psoriatic arthritis (PsA) and other spondyloarthritides (SpA).
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Affiliation(s)
- Elisa Assirelli
- Medicine and Rheumatology Unit, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Susanna Naldi
- Medicine and Rheumatology Unit, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Veronica Brusi
- Medicine and Rheumatology Unit, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Jacopo Ciaffi
- Medicine and Rheumatology Unit, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Lucia Lisi
- Medicine and Rheumatology Unit, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Luana Mancarella
- Medicine and Rheumatology Unit, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Federica Pignatti
- Medicine and Rheumatology Unit, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Lia Pulsatelli
- Laboratory of Immunorheumatology and Tissue Regeneration, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Cesare Faldini
- 1st Orthopedic and Traumatology Department, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences (DIBINEM), Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Francesco Ursini
- Medicine and Rheumatology Unit, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences (DIBINEM), Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Simona Neri
- Medicine and Rheumatology Unit, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
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Rodriguez Llorian E, Kopac N, Waliji LA, Borle K, Dragojlovic N, Elliott AM, Lynd LD. A Rapid Review on the Value of Biobanks Containing Genetic Information. VALUE IN HEALTH : THE JOURNAL OF THE INTERNATIONAL SOCIETY FOR PHARMACOECONOMICS AND OUTCOMES RESEARCH 2023; 26:1286-1295. [PMID: 36921900 DOI: 10.1016/j.jval.2023.02.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 01/20/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
OBJECTIVES Increasing access to health data through biobanks containing genetic information has the potential to expand the knowledge base and thereby improve screening, diagnosis, and treatment options for many diseases. Nevertheless, although privacy concerns and risks surrounding genetic data sharing are well documented, direct evidence in favor of the hypothesized benefits of data integration is scarce, which complicates decision making in this area. Therefore, the objective of this study is to summarize the available evidence on the research and clinical impacts of biobanks containing genetic information, so as to better understand how to quantify the value of expanding genomic data access. METHODS Using a rapid review methodology, we performed a search of MEDLINE/PubMed and Embase databases; and websites of biobanks and genomic initiatives published from 2010 to 2022. We classified findings into 11 indicators including outputs (a direct product of the biobank activities) and outcomes (changes in scientific and clinical capacity). RESULTS Of 8479 abstracts and 101 gray literature sources were reviewed, 96 records were included. Although most records did not report key indicators systematically, the available evidence concentrated on research indicators such as publications and gene-disorder association discoveries (63% of studies), followed by research infrastructure (26%), and clinical indicators (11%) such as supporting the diagnosis of individual patients. CONCLUSIONS Existing evidence on the benefits of biobanks is skewed toward easily quantifiable research outputs. Measuring a comprehensive set of outputs and outcomes inspired by value frameworks is necessary to generate better evidence on the benefits of genomic data sharing.
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Affiliation(s)
- Elisabet Rodriguez Llorian
- Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada.
| | - Nicola Kopac
- Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Louloua Ashikhusein Waliji
- Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Kennedy Borle
- Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Nick Dragojlovic
- Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Alison M Elliott
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Larry D Lynd
- Collaboration for Outcomes Research and Evaluation (CORE), Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada; Centre for Health Evaluation and Outcome Sciences (CHÉOS), St. Paul's Hospital, Vancouver, BC, Canada
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Remes Lenicov F, Fink NE. Ethical issues in the use of leftover samples and associated personal data obtained from diagnostic laboratories. Clin Chim Acta 2023; 548:117442. [PMID: 37308048 PMCID: PMC10257511 DOI: 10.1016/j.cca.2023.117442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/30/2023] [Accepted: 06/09/2023] [Indexed: 06/14/2023]
Abstract
Diagnostic laboratories are an integral part of the research ecosystem in biomedical sciences. Among other roles, laboratories are a source of clinically-characterized samples for research or diagnostic validation studies. Particularly during the COVID-19 pandemic, this process was entered by laboratories with different experience in the ethical management of human samples. The objective of this document is to present the current ethical framework regarding the use of leftover samples in clinical laboratories. Leftover samples are defined as the residue of a sample that has been obtained and used for clinical purposes, and would otherwise be discarded. Secondary use of samples typically demands institutional ethical oversight and informed consent by the participants, although the latter requirement could be exempted when the harm risks are sufficiently small. However, ongoing discussions have proposed that minimal risk is an insufficient argument to allow the use of samples without consent. In this article, we discuss both positions, to finally suggest that laboratories anticipating the secondary use of samples should consider the adoption of broad informed consent, or even the implementation of organized biobanking, in order to achieve higher standards of ethical compliance which would enhance their capacity to fulfill their role in the production of knowledge.
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Affiliation(s)
- Federico Remes Lenicov
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Universidad de Buenos Aires / CONICET, Buenos Aires, Argentina.
| | - Nilda E Fink
- Fundación Bioquímica Argentina, La Plata, Argentina.
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Domaradzki J, Czekajewska J, Walkowiak D. To donate or not to donate? Future healthcare professionals' opinions on biobanking of human biological material for research purposes. BMC Med Ethics 2023; 24:53. [PMID: 37481540 PMCID: PMC10363302 DOI: 10.1186/s12910-023-00930-z] [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: 01/10/2023] [Accepted: 07/11/2023] [Indexed: 07/24/2023] Open
Abstract
BACKGROUND Over the last few decades biobanks have been recognised as institutions that may revolutionise biomedical research and the development of personalised medicine. Poland, however, still lacks clear regulations regarding the running of biobanks and the conducting of biomedical research. While the awareness of the general public regarding biobanks is low, healthcare professions and medical students also lack basic knowledge regarding biobanks, and such ignorance may affect their support for biobanks. METHODS This study is aimed at assessing the knowledge and attitudes of future healthcare professionals towards the donation of human biological material for research purposes and is based on a sample of 865 Polish medical students at Poznań University of Medical Sciences. RESULTS This research has shown that the awareness of medical students' regarding biobanks is low. It has also shown that while the majority of future healthcare professionals enrolled in this study supported the idea of biobank research and declared themselves willing to donate, still many students felt ambivalent about the biobanking of human biological material for research purposes and expressed concerns over biobanking research. While the primarily motivation to participate in biobank research was the desire to help advance science and to develop innovative therapies, the most common reason for a refusal was the fear that the government, insurance companies or employers, might have access to the samples. Concerns over unethical use of samples and data safety were also prevalent. More than half of students opted for a study-specific model of consent and only a few opted for broad consent. CONCLUSIONS This research suggests that a lack of knowledge about biobanks, their role and activities may affect medical students' support for biobanks and their active participation in the collection and management of biospecimens for research purposes. Since in the future medical, nursing and pharmacy students will be involved in the collection, storage, testing and analysis of biospecimens from their patients, medical students in all professional fields should be trained regarding the concept, purposes and operational procedures of biobanks, as well as the ethical, legal and social implications of biobank research.
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Affiliation(s)
- Jan Domaradzki
- Department of Social Sciences and Humanities, Poznan University of Medical Sciences, Rokietnicka 7, St., Poznań, 60-806, Poland.
| | - Justyna Czekajewska
- Department of Social Sciences and Humanities, Poznan University of Medical Sciences, Rokietnicka 7, St., Poznań, 60-806, Poland
| | - Dariusz Walkowiak
- Department of Organization and Management in Health Care, Poznan University of Medical Sciences, Poznań, Poland
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Policiuc L, Nutu A, Zanoaga O, Mehterov N, Braicu C, Berindan-Neagoe I. Current aspects in biobanking for personalized oncology investigations and treatments. Med Pharm Rep 2023; 96:235-245. [PMID: 37577017 PMCID: PMC10419688 DOI: 10.15386/mpr-2647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 07/05/2023] [Indexed: 08/15/2023] Open
Abstract
Background/Aim A biobank is an organization that gathers, refines, preserves and provides access to biospecimens along with relevant clinical data that can be used in applied or clinical research. Biobanking is a critical component of the scientific foundation for personalized medicine; this implies the accessibility of high-quality human biospecimens, such as blood, tissue, and other body fluids, along with the patient clinical data that goes with them. Methods This paper summarizes the function of biobanks in oncology and the requirements for biobank development in translational and clinical research. Results Biobanks raise numerous ethical issues that government agencies address by enacting particular laws. To develop personalized medicine, biobanks are crucial, given that the availability of an extensive collection of patient samples with thoroughly annotated clinical and pathological data is an essential necessity. Also, data related to biobanking raises complex ethical, legal, and social issues, particularly concerning the protection of donor privacy and the appropriate use of collected samples. International standards have been developed to address these issues to ensure biobanking practices' quality, safety, and integrity. Conclusions Biobanking is vital in advancing biomedical research, supporting clinical applications, and enhancing our understanding of human health and disease. Using real-world data and biobanking can accelerate medical research, support personalized medicine initiatives, and improve patient care.
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Affiliation(s)
- Liliana Policiuc
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Andreea Nutu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Oana Zanoaga
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Nikolay Mehterov
- Research Institute, Medical University of Plovdiv, Plovdiv, Bulgaria
- Department of Dental Prosthetics, Faculty of Dental Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cornelia Braicu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
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Carney BC, Bailey JK, Powell HM, Supp DM, Travis TE. Scar Management and Dyschromia: A Summary Report from the 2021 American Burn Association State of the Science Meeting. J Burn Care Res 2023; 44:535-545. [PMID: 36752791 DOI: 10.1093/jbcr/irad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Indexed: 02/09/2023]
Abstract
Burn scars, and in particular, hypertrophic scars, are a challenging yet common outcome for survivors of burn injuries. In 2021, the American Burn Association brought together experts in burn care and research to discuss critical topics related to burns, including burn scars, at its State of the Science conference. Clinicians and researchers with burn scar expertise, as well as burn patients, industry representatives, and other interested stakeholders met to discuss issues related to burn scars and discuss priorities for future burn scar research. The various preventative strategies and treatment modalities currently utilized for burn scars were discussed, including relatively noninvasive therapies such as massage, compression, and silicone sheeting, as well as medical interventions such as corticosteroid injection and laser therapies. A common theme that emerged is that the efficacy of current therapies for specific patient populations is not clear, and further research is needed to improve upon these treatments and develop more effective strategies to suppress scar formation. This will necessitate quantitative analyses of outcomes and would benefit from creation of scar biobanks and shared data resources. In addition, outcomes of importance to patients, such as scar dyschromia, must be given greater attention by clinicians and researchers to improve overall quality of life in burn survivors. Herein we summarize the main topics of discussion from this meeting and offer recommendations for areas where further research and development are needed.
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Affiliation(s)
- Bonnie C Carney
- Firefighters' Burn and Surgical Research Laboratory, MedStar Health Research Institute, Washington, DC, USA
- Department of Biochemistry, Georgetown University School of Medicine, Washington, DC, USA
| | - John K Bailey
- Department of Surgery, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Heather M Powell
- The Ohio State University, Departments of Materials Science and Engineering and Biomedical Engineering, Columbus, OH, USA
- Scientific Staff, Shriners Children's Ohio, Dayton, OH, USA
| | - Dorothy M Supp
- Scientific Staff, Shriners Children's Ohio, Dayton, OH, USA
- The University of Cincinnati College of Medicine, Department of Surgery, Cincinnati, OH, USA
| | - Taryn E Travis
- Firefighters' Burn and Surgical Research Laboratory, MedStar Health Research Institute, Washington, DC, USA
- The Burn Center, MedStar Washington Hospital Center, Washington, DC, USA
- Department of Surgery, Georgetown University School of Medicine, Washington, DC, USA
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Weissinger SE, Georgantas NZ, Thierauf JC, Pellerin R, Gardecki E, Kühlinger S, Ritterhouse LL, Möller P, Lennerz JK. Slide-to-Slide Tissue Transfer and Array Assembly From Limited Samples for Comprehensive Molecular Profiling. J Transl Med 2023; 103:100062. [PMID: 36801639 PMCID: PMC10198954 DOI: 10.1016/j.labinv.2023.100062] [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: 10/12/2022] [Revised: 12/28/2022] [Accepted: 01/10/2023] [Indexed: 01/19/2023] Open
Abstract
Tissue microarrays (TMA) have become an important tool in high-throughput molecular profiling of tissue samples in the translational research setting. Unfortunately, high-throughput profiling in small biopsy specimens or rare tumor samples (eg, orphan diseases or unusual tumors) is often precluded owing to limited amounts of tissue. To overcome these challenges, we devised a method that allows tissue transfer and construction of TMAs from individual 2- to 5-μm sections for subsequent molecular profiling. We named the technique slide-to-slide (STS) transfer, and it requires a series of chemical exposures (so-called xylene-methacrylate exchange) in combination with rehydrated lifting, microdissection of donor tissues into multiple small tissue fragments (methacrylate-tissue tiles), and subsequent remounting on separate recipient slides (STS array slide). We developed the STS technique by assessing the efficacy and analytical performance using the following key metrics: (a) dropout rate, (b) transfer efficacy, (c) success rates using different antigen-retrieval methods, (d) success rates of immunohistochemical stains, (e) fluorescent in situ hybridization success rates, and (f) DNA and (g) RNA extraction yields from single slides, which all functioned appropriately. The dropout rate ranged from 0.7% to 6.2%; however, we applied the same STS technique successfully to fill these dropouts ("rescue" transfer). Hematoxylin and eosin assessment of donor slides confirmed a transfer efficacy of >93%, depending on the size of the tissue (range, 76%-100%). Fluorescent in situ hybridization success rates and nucleic acid yields were comparable with those of traditional workflows. In this study, we present a quick, reliable, and cost-effective method that offers the key advantages of TMAs and other molecular techniques-even when tissue is sparse. The perspectives of this technology in biomedical sciences and clinical practice are promising, given that it allows laboratories to create more data with less tissue.
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Affiliation(s)
- Stephanie E Weissinger
- Institute of Pathology, Alb Fils Clinics GmbH, Göppingen, Germany; Institute of Pathology, University Hospital Ulm, Ulm, Germany
| | - N Zeke Georgantas
- Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts
| | - Julia C Thierauf
- Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts
| | - Rebecca Pellerin
- Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts
| | - Emma Gardecki
- Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts
| | | | - Lauren L Ritterhouse
- Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts
| | - Peter Möller
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
| | - Jochen K Lennerz
- Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts.
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50
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Eccher A, Scarpa A, Dei Tos AP. Impact of a centralized archive for pathology laboratories on the health system. Pathol Res Pract 2023; 245:154488. [PMID: 37116365 DOI: 10.1016/j.prp.2023.154488] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 04/30/2023]
Abstract
The pathology archive of any hospital is likely to contain tens of thousands of slides and formalin-fixed and paraffin-embedded (FFPE) blocks, with their number constantly increasing. As a result, serious space and management issues are created. There has always been a favorable location for the pathology laboratory to rapidly and efficiently collect specimens and to meet the different service requirements of clinicians and patients. However, archiving may be one of the most neglected issues in the planning of spaces and activities, so much so that many laboratories are currently in trouble and looking for space inside and outside their hospitals. Another crucial issue is related to the environmental conditions of the identified preservation place, which, based on their characteristics, probably provide suboptimal habitats in most cases. For FFPE blocks, controlled temperature (<27 °C) and humidity (>30% and <70%) are recommended, with control systems for parasite infestation. For glass slides, systems suitable for guaranteeing their safety, traceability and conservation suitable for possible revision are recommended. The aim of this position paper is to outline the issues that currently exist in archives and to suggest a rational health policy solution to overcome the problems raised.
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Affiliation(s)
- Albino Eccher
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy.
| | - Aldo Scarpa
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Angelo Paolo Dei Tos
- Surgical Pathology & Cytopathology Unit, Department of Medicine - DIMED, University of Padua, Padua, Italy
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