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Verscheure E, Stierum R, Schlünssen V, Lund Würtz AM, Vanneste D, Kogevinas M, Harding BN, Broberg K, Zienolddiny-Narui S, Erdem JS, Das MK, Makris KC, Konstantinou C, Andrianou X, Dekkers S, Morris L, Pronk A, Godderis L, Ghosh M. Characterization of the internal working-life exposome using minimally and non-invasive sampling methods - a narrative review. ENVIRONMENTAL RESEARCH 2023; 238:117001. [PMID: 37683788 DOI: 10.1016/j.envres.2023.117001] [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: 04/13/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023]
Abstract
During recent years, we are moving away from the 'one exposure, one disease'-approach in occupational settings and towards a more comprehensive approach, taking into account the totality of exposures during a life course by using an exposome approach. Taking an exposome approach however is accompanied by many challenges, one of which, for example, relates to the collection of biological samples. Methods used for sample collection in occupational exposome studies should ideally be minimally invasive, while at the same time sensitive, and enable meaningful repeated sampling in a large population and over a longer time period. This might be hampered in specific situations e.g., people working in remote areas, during pandemics or with flexible work hours. In these situations, using self-sampling techniques might offer a solution. Therefore, our aim was to identify existing self-sampling techniques and to evaluate the applicability of these techniques in an occupational exposome context by conducting a literature review. We here present an overview of current self-sampling methodologies used to characterize the internal exposome. In addition, the use of different biological matrices was evaluated and subdivided based on their level of invasiveness and applicability in an occupational exposome context. In conclusion, this review and the overview of self-sampling techniques presented herein can serve as a guide in the design of future (occupational) exposome studies while circumventing sample collection challenges associated with exposome studies.
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Affiliation(s)
- Eline Verscheure
- Department of Public Health and Primary Care, Centre for Environment and Health, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Rob Stierum
- Netherlands Organisation for Applied Scientific Research TNO, Risk Analysis for Products in Development, Utrecht, the Netherlands
| | - Vivi Schlünssen
- Department of Public Health, Research unit for Environment, Occupation and Health, Danish Ramazzini Centre, Aarhus University, Aarhus, Denmark
| | - Anne Mette Lund Würtz
- Department of Public Health, Research unit for Environment, Occupation and Health, Danish Ramazzini Centre, Aarhus University, Aarhus, Denmark
| | - Dorian Vanneste
- Department of Public Health and Primary Care, Centre for Environment and Health, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Manolis Kogevinas
- Environment and Health over the Lifecourse Program, ISGlobal, Barcelona, Spain
| | - Barbara N Harding
- Environment and Health over the Lifecourse Program, ISGlobal, Barcelona, Spain
| | - Karin Broberg
- Division of Occupational and Environmental Medicine, Lund University, Lund, Sweden; Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Mrinal K Das
- National Institute of Occupational Health, Oslo, Norway
| | - Konstantinos C Makris
- Cyprus International Institute for Environmental and Public Health, Cyprus University of Technology, Limassol, Cyprus
| | - Corina Konstantinou
- Cyprus International Institute for Environmental and Public Health, Cyprus University of Technology, Limassol, Cyprus
| | - Xanthi Andrianou
- Cyprus International Institute for Environmental and Public Health, Cyprus University of Technology, Limassol, Cyprus
| | - Susan Dekkers
- Netherlands Organisation for Applied Scientific Research TNO, Risk Analysis for Products in Development, Utrecht, the Netherlands
| | | | - Anjoeka Pronk
- Netherlands Organisation for Applied Scientific Research TNO, Risk Analysis for Products in Development, Utrecht, the Netherlands
| | - Lode Godderis
- Department of Public Health and Primary Care, Centre for Environment and Health, Katholieke Universiteit Leuven, Leuven, Belgium; Idewe, External Service for Prevention and Protection at work, Heverlee, Belgium.
| | - Manosij Ghosh
- Department of Public Health and Primary Care, Centre for Environment and Health, Katholieke Universiteit Leuven, Leuven, Belgium.
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Zhang Y, Jin Y, Wang H, He L, Zhang Y, Liu Q, Xin Y, Li X. Identification of Genes Associated with Decreasing Abundance of Monocytes in Long-Term Peritoneal Dialysis Patients. Int J Gen Med 2023; 16:5017-5030. [PMID: 37942472 PMCID: PMC10629397 DOI: 10.2147/ijgm.s435041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/19/2023] [Indexed: 11/10/2023] Open
Abstract
Purpose Chronic kidney disease (CKD) will become an end-stage renal disease (ESRD) at stage 5. Peritoneal dialysis (PD) is required for renal replacement therapy. This study aims to identify monocytes-related genes in peritoneal cells from long-term PD (LPD) patients and short-term PD (SPD) patients. Methods Bulk RNA-seq data (GSE125498 dataset) and ScRNA-seq data (GSE130888) were downloaded to identify differentially expressed genes, monocytes-related genes, and monocytes marker genes in LPD patients. Immune infiltration was analyzed in the GSE125498 dataset. Core genes associated with monocytes changes were screened out, followed by functional analysis and expression validation using RT-PCR. Results Monocytes are the most abundant immune cell in PD. The number of monocytes was remarkably decreased in LPD compared with SPD. A total of 16 up-regulated core genes negatively correlated with the abundance of monocytes were obtained in LPD. The expression of 16 core genes was lower in monocyte clusters than that in other cell clusters. In addition, LCK, CD3G, CD3E, CD3D, and LAT were involved in the signaling pathways of Th1 and Th2 cell differentiation, T cell receptor signaling pathway, and Th17 cell differentiation. CD2 was involved in hematopoietic cell lineage signaling pathway. Conclusion Identification of monocytes related-genes and related signaling pathways could be helpful in understanding the molecular mechanism of monocytes changes during PD.
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Affiliation(s)
- Yinghui Zhang
- Department of Nephrology, General Hospital of Northern Theater Command, Shenyang, Liaoning Province, People’s Republic of China
| | - Yanhua Jin
- Department of Nephrology, General Hospital of Northern Theater Command, Shenyang, Liaoning Province, People’s Republic of China
| | - Huan Wang
- Department of Nephrology, General Hospital of Northern Theater Command, Shenyang, Liaoning Province, People’s Republic of China
| | - Long He
- Organ Transplant Center, General Hospital of Northern Theater Command, Shenyang, Liaoning Province, People’s Republic of China
| | - Yanning Zhang
- Department of Nephrology, General Hospital of Northern Theater Command, Shenyang, Liaoning Province, People’s Republic of China
| | - Qi Liu
- Department of Nephrology, General Hospital of Northern Theater Command, Shenyang, Liaoning Province, People’s Republic of China
| | - Yu Xin
- Department of Nephrology, General Hospital of Northern Theater Command, Shenyang, Liaoning Province, People’s Republic of China
| | - Xueyu Li
- Nursing Department, General Hospital of Northern Theater Command, Shenyang, Liaoning Province, People’s Republic of China
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Yeh H. Applications of Transcriptomics in the Research of Antibody-Mediated Rejection in Kidney Transplantation: Progress and Perspectives. Organogenesis 2022; 18:2131357. [PMID: 36259540 PMCID: PMC9586696 DOI: 10.1080/15476278.2022.2131357] [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] [Indexed: 02/09/2023] Open
Abstract
Antibody-mediated rejection (ABMR) is the major cause of chronic allograft dysfunction and loss in kidney transplantation. The immunological mechanisms of ABMR that have been featured in the latest studies indicate a highly complex interplay between various immune and nonimmune cell types. Clinical diagnostic standards have long been criticized for being arbitrary and the lack of accuracy. Transcriptomic approaches, including microarray and RNA sequencing of allograft biopsies, enable the identification of differential gene expression and the continuous improvement of diagnostics. Given that conventional bulk transcriptomic approaches only reflect the average gene expression but not the status at the single-cell level, thereby ignoring the heterogeneity of the transcriptome across individual cells, single-cell RNA sequencing is rising as a powerful tool to provide a high-resolution transcriptome map of immune cells, which allows the elucidation of the pathogenesis and may facilitate the development of novel strategies for clinical treatment of ABMR.
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Affiliation(s)
- Hsuan Yeh
- Division of Renal-Electrolyte, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA,CONTACT Hsuan Yeh S976 Scaife Hall 3550 Terrace Street Pittsburgh, PA 15261
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Lubetzky ML, Salinas T, Schwartz JE, Suthanthiran M. Urinary Cell mRNA Profiles Predictive of Human Kidney Allograft Status. Clin J Am Soc Nephrol 2021; 16:1565-1577. [PMID: 33906907 PMCID: PMC8499006 DOI: 10.2215/cjn.14010820] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Immune monitoring of kidney allograft recipients and personalized therapeutics may help reach the aspirational goal of "one transplant for life." The invasive kidney biopsy procedure, the diagnostic tool of choice, has become safer and the biopsy classification more refined. Nevertheless, biopsy-associated complications, interobserver variability in biopsy specimen scoring, and costs continue to be significant concerns. The dynamics of the immune repertoire make frequent assessments of allograft status necessary, but repeat biopsies of the kidney are neither practical nor safe. To address the existing challenges, we developed urinary cell mRNA profiling and investigated the diagnostic, prognostic, and predictive accuracy of absolute levels of a hypothesis-based panel of mRNAs encoding immunoregulatory proteins. Enabled by our refinements of the PCR assay and by investigating mechanistic hypotheses, our single-center studies identified urinary cell mRNAs associated with T cell-mediated rejection, antibody-mediated rejection, interstitial fibrosis and tubular atrophy, and BK virus nephropathy. In the multicenter National Institutes of Health Clinical Trials in Organ Transplantation-04, we discovered and validated a urinary cell three-gene signature of T-cell CD3 ε chain mRNA, interferon gamma inducible protein 10 (IP-10) mRNA, and 18s ribosomal RNA that is diagnostic of subclinical acute cellular rejection and acute cellular rejection and prognostic of acute cellular rejection and graft function. The trajectory of the signature score remained flat and below the diagnostic threshold for acute cellular rejection in the patients with no rejection biopsy specimens, whereas a sharp rise was observed during the weeks before the biopsy specimen that showed acute cellular rejection. Our RNA sequencing and bioinformatics identified kidney allograft biopsy specimen gene signatures of acute rejection to be enriched in urinary cells matched to acute rejection biopsy specimens. The urinary cellular landscape was more diverse and more enriched for immune cell types compared with kidney allograft biopsy specimens. Urinary cell mRNA profile-guided clinical trials are needed to evaluate their value compared with current standard of care.
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Affiliation(s)
- Michelle L. Lubetzky
- Division of Nephrology and Hypertension, Weill Cornell Department of Medicine, New York, New York,Department of Transplantation Medicine, New York–Presbyterian Hospital, New York, New York
| | - Thalia Salinas
- Division of Nephrology and Hypertension, Weill Cornell Department of Medicine, New York, New York,Department of Transplantation Medicine, New York–Presbyterian Hospital, New York, New York
| | - Joseph E. Schwartz
- Division of Nephrology and Hypertension, Weill Cornell Department of Medicine, New York, New York,Department of Transplantation Medicine, New York–Presbyterian Hospital, New York, New York,Department of Psychiatry and Behavioral Sciences, Stony Brook Renaissance School of Medicine, Stony Brook, New York
| | - Manikkam Suthanthiran
- Division of Nephrology and Hypertension, Weill Cornell Department of Medicine, New York, New York,Department of Transplantation Medicine, New York–Presbyterian Hospital, New York, New York
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Dissecting the human kidney allograft transcriptome: single-cell RNA sequencing. Curr Opin Organ Transplant 2021; 26:43-51. [PMID: 33315769 DOI: 10.1097/mot.0000000000000840] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE OF REVIEW Single-cell RNA sequencing (scRNA-seq) has provided opportunities to interrogate kidney allografts at a hitherto unavailable molecular level of resolution. Understanding of this technology is essential to better appreciate the relevant biomedical literature. RECENT FINDINGS Sequencing is a technique to determine the order of nucleotides in a segment of RNA or DNA. RNA-seq of kidney allograft tissues has revealed novel mechanistic insights but does not provide information on individual cell types and cell states. scRNA-seq enables to study the transcriptome of individual cells and assess the transcriptional differences and similarities within a population of cells. Initial studies on rejecting kidney allograft tissues in humans have identified the transcriptional profile of the active players of the innate and adaptive immune system. Application of scRNA-seq in a preclinical model of kidney transplantation has revealed that allograft-infiltrating myeloid cells follow a trajectory of differentiation from monocytes to proinflammatory macrophages and exhibit distinct interactions with kidney allograft parenchymal cells; myeloid cell expression of Axl played a major role in promoting intragraft myeloid cell and T-cell differentiation. SUMMARY The current review discusses the technical aspects of scRNA-seq and summarizes the application of this technology to dissect the human kidney allograft transcriptome.
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