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Franchini F, Kusejko K, Marzolini C, Tellenbach C, Rossi S, Stampf S, Koller M, Stoyanov J, Möller B, Leichtle AB. Collaborative Challenges of Multi-Cohort Projects in Pharmacogenetics—Why Time Is Essential for Meaningful Collaborations. JMIR Form Res 2022; 6:e36759. [PMID: 35976179 PMCID: PMC9562084 DOI: 10.2196/36759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/02/2022] [Accepted: 08/17/2022] [Indexed: 02/04/2023] Open
Abstract
Multi-cohort projects in medicine provide an opportunity to investigate scientific questions beyond the boundaries of a single institution and endeavor to increase the sample size for obtaining more reliable results. However, the complications of these kinds of collaborations arise during management, with many administrative hurdles. Hands-on approaches and lessons learned from previous collaborations provide solutions for optimized collaboration models. Here, we use our experience in running PGX-link, a Swiss multi-cohort project, to show the strategy we used to tackle different challenges from project setup to obtaining the relevant permits, including ethics approval. We set PGX-link in an international context because our struggles were similar to those encountered during the SYNCHROS (SYNergies for Cohorts in Health: integrating the ROle of all Stakeholders) project. We provide ad hoc solutions for cohorts, general project management strategies, and suggestions for unified protocols between cohorts that would ease current management hurdles. Project managers are not necessarily familiar with medical projects, and even if they are, they are not aware of the intricacies behind decision-making and consequently, of the time needed to set up multi-cohort collaborations. This paper is meant to be a brief overview of what we experienced with our multi-cohort project and provides the necessary practices for future managers.
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Affiliation(s)
- Filippo Franchini
- University Institute of Clinical Chemistry, Inselspital - Bern University Hospital, University of Bern, Bern, Switzerland
| | - Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zürich, Switzerland
| | - Catia Marzolini
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | | | - Simona Rossi
- Swiss Transplant Cohort Study, Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland
| | - Susanne Stampf
- Swiss Transplant Cohort Study, Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland
| | - Michael Koller
- Swiss Transplant Cohort Study, Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland
| | - Jivko Stoyanov
- Swiss Paraplegic Research, Nottwil, Switzerland
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Burkhard Möller
- University Clinics of Rheumatology and Immunology, Inselspital - Bern University Hospital and University of Bern, Bern, Switzerland
| | - Alexander Benedikt Leichtle
- University Institute of Clinical Chemistry, Inselspital - Bern University Hospital, University of Bern, Bern, Switzerland
- Center for Artificial Intelligence in Medicine, University of Bern, Bern, Switzerland
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Abstract
Over the past four decades, research on the natural history of HIV infection has described how HIV wreaks havoc on human immunity and causes AIDS. HIV host genomic research, which aims to understand how human genetic variation affects our response to HIV infection, has progressed from early candidate gene studies to recent multi-omic efforts, benefiting from spectacular advances in sequencing technology and data science. In addition to invading cells and co-opting the host machinery for replication, HIV also stably integrates into our own genome. The study of the complex interactions between the human and retroviral genomes has improved our understanding of pathogenic mechanisms and suggested novel preventive and therapeutic approaches against HIV infection.
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Affiliation(s)
- Paul J. McLaren
- grid.415368.d0000 0001 0805 4386National HIV and Retrovirology Laboratory at the JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB Canada ,grid.21613.370000 0004 1936 9609Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB Canada
| | - Jacques Fellay
- grid.5333.60000000121839049School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland ,grid.419765.80000 0001 2223 3006Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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Goyal R, Singhal PC. APOL1 risk variants and the development of HIV-associated nephropathy. FEBS J 2020; 288:5586-5597. [PMID: 33340240 DOI: 10.1111/febs.15677] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 12/08/2020] [Accepted: 12/16/2020] [Indexed: 01/03/2023]
Abstract
HIV-associated nephropathy (HIVAN) remains a concern among untreated HIV patients, notably of African descent, as patients can reach end-stage renal disease within 3 years. Two variants (G1 and G2) of the APOL1 gene, common in African populations to protect against African sleeping sickness, have been associated with an increased risk of several glomerular disorders including HIVAN, hypertension-attributed chronic kidney disease, and idiopathic focal segmental glomerulosclerosis and are accordingly named renal risk variants (RRVs). This review examines the mechanisms by which APOL1 RRVs drive glomerular injury in the setting of HIV infection and their potential application to patient management. Innate antiviral mechanisms activated by chronic HIV infection, especially those involving type 1 interferons, are of particular interest as they have been shown to upregulate APOL1 expression. Additionally, the downregulation of miRNA 193a (a repressor of APOL1) is also associated with the upregulation of APOL1. Interestingly, glomerular damage affected by APOL1 RRVs is caused by both loss- and gain-of-function changes in the protein, explicitly characterizing these effects. Their intracellular localization offers a further understanding of the nuances of APOL1 variant effects in promoting renal disease. Finally, although APOL1 variants have been recognized as a critical genetic player in mediating kidney disease, there are significant gaps in their application to patient management for screening, diagnosis, and treatment.
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Affiliation(s)
- Rohan Goyal
- SUNY Downstate Health Sciences University, New York, NY, USA
| | - Pravin C Singhal
- Institute of Molecular Medicine, Feinstein Institute for Medical Research and Zucker School of Medicine at Hofstra-Northwell, Manhasset, NY, USA
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de Seigneux S, Lucas GM. Renal injury and human immunodeficiency virus: what remains after 30 years? Nephrol Dial Transplant 2020; 35:555-557. [PMID: 31407789 PMCID: PMC7139202 DOI: 10.1093/ndt/gfz162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/10/2019] [Indexed: 12/21/2022] Open
Affiliation(s)
- Sophie de Seigneux
- Service and Laboratory of Nephrology, PHYME and Medicine Department, University Hospital of Geneva, Geneva, Switzerland
| | - Gregory M Lucas
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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