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Wen Y, Vechetti IJ, Leng D, Alimov AP, Valentino TR, Zhang XD, McCarthy JJ, Peterson CA. Early transcriptomic signatures and biomarkers of renal damage due to prolonged exposure to embedded metal. Cell Biol Toxicol 2023; 39:2861-2880. [PMID: 37058270 DOI: 10.1007/s10565-023-09806-9] [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: 06/14/2022] [Accepted: 03/24/2023] [Indexed: 04/15/2023]
Abstract
BACKGROUND Prolonged exposure to toxic heavy metals leads to deleterious health outcomes including kidney injury. Metal exposure occurs through both environmental pathways including contamination of drinking water sources and from occupational hazards, including the military-unique risks from battlefield injuries resulting in retained metal fragments from bullets and blast debris. One of the key challenges to mitigate health effects in these scenarios is to detect early insult to target organs, such as the kidney, before irreversible damage occurs. METHODS High-throughput transcriptomics (HTT) has been recently demonstrated to have high sensitivity and specificity as a rapid and cost-effective assay for detecting tissue toxicity. To better understand the molecular signature of early kidney damage, we performed RNA sequencing (RNA-seq) on renal tissue using a rat model of soft tissue-embedded metal exposure. We then performed small RNA-seq analysis on serum samples from the same animals to identify potential miRNA biomarkers of kidney damage. RESULTS We found that metals, especially lead and depleted uranium, induce oxidative damage that mainly cause dysregulated mitochondrial gene expression. Utilizing publicly available single-cell RNA-seq datasets, we demonstrate that deep learning-based cell type decomposition effectively identified cells within the kidney that were affected by metal exposure. By combining random forest feature selection and statistical methods, we further identify miRNA-423 as a promising early systemic marker of kidney injury. CONCLUSION Our data suggest that combining HTT and deep learning is a promising approach for identifying cell injury in kidney tissue. We propose miRNA-423 as a potential serum biomarker for early detection of kidney injury.
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Affiliation(s)
- Yuan Wen
- Department of Physical Therapy, College of Health Sciences, University of Kentucky, Lexington, KY, USA.
- Center for Muscle Biology, University of Kentucky, Lexington, KY, USA.
| | - Ivan J Vechetti
- Department of Nutrition and Health Sciences, College of Education and Human Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Dongliang Leng
- Faculty of Health Sciences, CRDA, University of Macau, Taipa, Macau, China
| | - Alexander P Alimov
- Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Taylor R Valentino
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
| | - Xiaohua D Zhang
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, KY, USA
| | - John J McCarthy
- Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Charlotte A Peterson
- Department of Physical Therapy, College of Health Sciences, University of Kentucky, Lexington, KY, USA
- Center for Muscle Biology, University of Kentucky, Lexington, KY, USA
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Pandiri AR, Auerbach SS, Stevens JL, Blomme EAG. Toxicogenomics Approaches to Address Toxicity and Carcinogenicity in the Liver. Toxicol Pathol 2023; 51:470-481. [PMID: 38288963 PMCID: PMC11014763 DOI: 10.1177/01926233241227942] [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] [Indexed: 04/13/2024]
Abstract
Toxicogenomic technologies query the genome, transcriptome, proteome, and the epigenome in a variety of toxicological conditions. Due to practical considerations related to the dynamic range of the assays, sensitivity, cost, and technological limitations, transcriptomic approaches are predominantly used in toxicogenomics. Toxicogenomics is being used to understand the mechanisms of toxicity and carcinogenicity, evaluate the translational relevance of toxicological responses from in vivo and in vitro models, and identify predictive biomarkers of disease and exposure. In this session, a brief overview of various transcriptomic technologies and practical considerations related to experimental design was provided. The advantages of gene network analyses to define mechanisms were also discussed. An assessment of the utility of toxicogenomic technologies in the environmental and pharmaceutical space showed that these technologies are being increasingly used to gain mechanistic insights and determining the translational relevance of adverse findings. Within the environmental toxicology area, there is a broader regulatory consideration of benchmark doses derived from toxicogenomics data. In contrast, these approaches are mainly used for internal decision-making in pharmaceutical development. Finally, the development and application of toxicogenomic signatures for prediction of apical endpoints of regulatory concern continues to be area of intense research.
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Affiliation(s)
- Arun R Pandiri
- National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Scott S Auerbach
- National Institute of Environmental Health Sciences, Durham, North Carolina, USA
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Thompson CM, Heintz MM, Wolf JC, Cheru R, Haws LC, Cullen JM. Assessment of Mouse Liver Histopathology Following Exposure to HFPO-DA With Emphasis on Understanding Mechanisms of Hepatocellular Death. Toxicol Pathol 2023; 51:4-14. [PMID: 36987989 PMCID: PMC10278389 DOI: 10.1177/01926233231159078] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Ammonium 2,3,3,3-tetrafluoro-2-(heptafluoropropoxy)-propanoate (HFPO-DA) is a short chain member of per- and polyfluoroalkyl substances (PFAS). To better understand the relevance of histopathological effects seen in livers of mice exposed to HFPO-DA for human health risk assessment, histopathological effects were summarized from hematoxylin and eosin (H&E)-stained sections in several repeat-dose toxicity studies in mice. Findings across studies revealed histopathological changes consistent with peroxisomal proliferation, whereas two reports of steatosis could not be confirmed in the published figures. In addition, mechanisms of hepatocellular death were assessed in H&E sections as well as with the apoptotic marker cleaved caspase-3 (CCasp3) in newly cut sections from archived liver blocks from select studies. A comparison of serially CCasp3 immunolabeled and H&E-stained sections revealed that mechanisms of hepatocellular death cannot be clearly discerned in H&E-stained liver sections alone as several examples of putatively necrotic cells were positive for CCasp3. Published whole genome transcriptomic data were also reevaluated for enrichment of various forms of hepatocellular death in response to HFPO-DA, which revealed enrichment of apoptosis and autophagy, but not ferroptosis, pyroptosis, or necroptosis. These morphological and molecular findings are consistent with transcriptomic evidence for peroxisome proliferator-activated receptor alpha (PPARα) signaling in HFPO-DA exposed mice.
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Affiliation(s)
| | | | - Jeffrey C. Wolf
- Experimental Pathology Laboratories, Sterling, Virginia, USA
| | - Roza Cheru
- Experimental Pathology Laboratories, Sterling, Virginia, USA
| | | | - John M. Cullen
- North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, USA
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Yen NTH, Park SM, Thu VTA, Phat NK, Cho YS, Yoon S, Shin JG, Kim DH, Oh JH, Long NP. Genome-wide gene expression analysis reveals molecular insights into the drug-induced toxicity of nephrotoxic agents. Life Sci 2022; 306:120801. [PMID: 35850247 DOI: 10.1016/j.lfs.2022.120801] [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: 04/26/2022] [Revised: 06/30/2022] [Accepted: 07/09/2022] [Indexed: 11/17/2022]
Abstract
Drug-induced nephrotoxicity is frequently reported. However, the mechanisms underlying nephrotoxic medications and their overlapping molecular events, which might have therapeutic value, are unclear. We performed a genome-wide analysis of gene expression and a gene set enrichment analysis to identify common and unique pathways associated with the toxicity of colistin, ifosfamide, indomethacin, and puromycin. Rats were randomly allocated into the treatment or control group. The treatment group received a toxic dose once daily of each investigated drug for 1 week. Differentially expressed genes were found in the drug-treated kidney and liver compared to the control, except for colistin in the liver. Upregulated pathways were mainly related to cell death, cell cycle, protein synthesis, and immune response modulation in the kidney. Cell cycle was upregulated by all drugs. Downregulated pathways were associated with carbon metabolism, amino acid metabolism, and fatty acid metabolism. Indomethacin, colistin, and puromycin shared the most altered pathways in the kidney. Ifosfamide and indomethacin affected molecular processes greatly in the liver. Our findings provide insight into the mechanisms underlying the renal and hepatic adverse effects of the four drugs. Further investigation should explore the combinatory drug therapies that attenuate the toxic effects and maximize the effectiveness of nephrotoxic drugs.
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Affiliation(s)
- Nguyen Thi Hai Yen
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan 614-735, Republic of Korea; Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan 614-735, Republic of Korea
| | - Se-Myo Park
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon 34114, Republic of Korea
| | - Vo Thuy Anh Thu
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan 614-735, Republic of Korea; Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan 614-735, Republic of Korea
| | - Nguyen Ky Phat
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan 614-735, Republic of Korea; Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan 614-735, Republic of Korea
| | - Yong-Soon Cho
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan 614-735, Republic of Korea; Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan 614-735, Republic of Korea
| | - Seokjoo Yoon
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon 34114, Republic of Korea
| | - Jae-Gook Shin
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan 614-735, Republic of Korea; Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan 614-735, Republic of Korea
| | - Dong Hyun Kim
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan 614-735, Republic of Korea
| | - Jung-Hwa Oh
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon 34114, Republic of Korea.
| | - Nguyen Phuoc Long
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan 614-735, Republic of Korea; Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan 614-735, Republic of Korea.
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Current Therapeutic Landscape and Safety Roadmap for Targeting the Aryl Hydrocarbon Receptor in Inflammatory Gastrointestinal Indications. Cells 2022; 11:cells11101708. [PMID: 35626744 PMCID: PMC9139855 DOI: 10.3390/cells11101708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/30/2022] [Accepted: 05/16/2022] [Indexed: 02/07/2023] Open
Abstract
Target modulation of the AhR for inflammatory gastrointestinal (GI) conditions holds great promise but also the potential for safety liabilities both within and beyond the GI tract. The ubiquitous expression of the AhR across mammalian tissues coupled with its role in diverse signaling pathways makes development of a “clean” AhR therapeutically challenging. Ligand promiscuity and diversity in context-specific AhR activation further complicates targeting the AhR for drug development due to limitations surrounding clinical translatability. Despite these concerns, several approaches to target the AhR have been explored such as small molecules, microbials, PROTACs, and oligonucleotide-based approaches. These various chemical modalities are not without safety liabilities and require unique de-risking strategies to parse out toxicities. Collectively, these programs can benefit from in silico and in vitro methodologies that investigate specific AhR pathway activation and have the potential to implement thresholding parameters to categorize AhR ligands as “high” or “low” risk for sustained AhR activation. Exploration into transcriptomic signatures for AhR safety assessment, incorporation of physiologically-relevant in vitro model systems, and investigation into chronic activation of the AhR by structurally diverse ligands will help address gaps in our understanding regarding AhR-dependent toxicities. Here, we review the role of the AhR within the GI tract, novel therapeutic modality approaches to target the AhR, key AhR-dependent safety liabilities, and relevant strategies that can be implemented to address drug safety concerns. Together, this review discusses the emerging therapeutic landscape of modalities targeting the AhR for inflammatory GI indications and offers a safety roadmap for AhR drug development.
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Christopher Corton J, Mitchell CA, Auerbach S, Bushel JP, Ellinger-Ziegelbauer H, Escobar PA, Froetschl R, Harrill AH, Johnson K, Klaunig JE, Pandiri AR, Podtelezhnikov AA, Rager JE, Tanis KQ, van der Laan JW, Vespa A, Yauk CL, Pettit SD, Sistare FD. A Collaborative Initiative to Establish Genomic Biomarkers for Assessing Tumorigenic Potential to Reduce Reliance on Conventional Rodent Carcinogenicity Studies. Toxicol Sci 2022; 188:4-16. [PMID: 35404422 PMCID: PMC9238304 DOI: 10.1093/toxsci/kfac041] [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] [Indexed: 11/24/2022] Open
Abstract
There is growing recognition across broad sectors of the scientific community that use of genomic biomarkers has the potential to reduce the need for conventional rodent carcinogenicity studies of industrial chemicals, agrochemicals, and pharmaceuticals through a weight-of-evidence approach. These biomarkers fall into 2 major categories: (1) sets of gene transcripts that can identify distinct tumorigenic mechanisms of action; and (2) cancer driver gene mutations indicative of rapidly expanding growth-advantaged clonal cell populations. This call-to-action article describes a collaborative approach launched to develop and qualify biomarker gene expression panels that measure widely accepted molecular pathways linked to tumorigenesis and their activation levels to predict tumorigenic doses of chemicals from short-term exposures. Growing evidence suggests that application of such biomarker panels in short-term exposure rodent studies can identify both tumorigenic hazard and tumorigenic activation levels for chemical-induced carcinogenicity. In the future, this approach will be expanded to include methodologies examining mutations in key cancer driver gene mutation hotspots as biomarkers of both genotoxic and nongenotoxic chemical tumor risk. Analytical, technical, and biological validation studies of these complementary genomic tools are being undertaken by multisector and multidisciplinary collaborative teams within the Health and Environmental Sciences Institute. Success from these efforts will facilitate the transition from current heavy reliance on conventional 2-year rodent carcinogenicity studies to more rapid animal- and resource-sparing approaches for mechanism-based carcinogenicity evaluation supporting internal and regulatory decision-making.
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Affiliation(s)
- J Christopher Corton
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, NC, USA
| | | | - Scott Auerbach
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - J Pierre Bushel
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | | | - Patricia A Escobar
- Safety Assessment and Laboratory Animal Resources, Merck Sharp & Dohme Corp, West Point, PA, USA
| | - Roland Froetschl
- BfArM-Bundesinstitut für Arzneimittel und Medizinprodukte, Federal Institute for Drugs and Medical Devices, Kurt-Georg-Kiesinger-Allee 3, Bonn, Germany
| | - Alison H Harrill
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | | | - James E Klaunig
- Laboratory of Investigative Toxicology and Pathology, Department of Environmental and Occupational Health, Indiana School of Public Health, Indiana University, Bloomington, IN, USA
| | - Arun R Pandiri
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | | | - Julia E Rager
- The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Keith Q Tanis
- Safety Assessment and Laboratory Animal Resources, Merck Sharp & Dohme Corp, West Point, PA, USA
| | - Jan Willem van der Laan
- Section on Pharmacology, Toxicology and Kinetics, Medicines Evaluation Board, Utrecht, The Netherlands
| | - Alisa Vespa
- Therapeutic Products Directorate, Health Canada, Ottawa, Canada
| | - Carole L Yauk
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Syril D Pettit
- Health and Environmental Sciences Institute, Washington, DC, USA
| | - Frank D Sistare
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
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Mandal M, Madeira M, Amin R, Buevich AV, Cheng A, Labroli M, Liu X, Acton J, Pio B, Basso A, Chobanian H, Dong G, Dropinski J, Guo Y, Guo Z, Kurowski S, Korfmacher W, Lee S, Meng D, Ondeyka D, Yang Z, Zhang R, Wei H, Wu Z, Zhang F, Wollenberg G, Biftu T, Greenlee WJ, Chintala M, Maletic M, Zhu Z. Lead Optimization to Advance Protease-Activated Receptor-1 Antagonists in Early Discovery. J Med Chem 2022; 65:5575-5592. [DOI: 10.1021/acs.jmedchem.1c02048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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8
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Vlasakova K, Bourque J, Bailey WJ, Patel S, Besteman EG, Gonzalez RJ, Sistare FD, Glaab WE. Universal Accessible Biomarkers of Drug-Induced Tissue Injury and Systemic Inflammation in Rat: Performance Assessment of TIMP-1, A2M, AGP, NGAL and Albumin. Toxicol Sci 2022; 187:219-233. [PMID: 35285504 DOI: 10.1093/toxsci/kfac030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The ability to monitor for general drug-induced tissue injury (DITI) or systemic inflammation in any tissue using blood-based accessible biomarkers would provide a valuable tool in early exploratory animal studies to understand potential drug liabilities. Here we describe the evaluation of four biomarkers of tissue remodeling and inflammation [α2-macroglobin (A2M), α1-acid glycoprotein (AGP), neutrophil gelatinase-associated lipocalin (NGAL) and tissue inhibitor of metalloproteinases (TIMP-1)] as well as the traditional serum parameter albumin as potential blood-based biomarkers of DITI and systemic inflammatory response (SIR). Biomarker performance was assessed in 51 short-term rat in vivo studies with various end-organ toxicities or SIR and receiver operator characteristic (ROC) curves were generated to compare relative performances. All four biomarkers performed well in their ability to detect DITI and SIR with an area under the curve (AUC) of 0.82 - 0.78, however TIMP-1 achieved the best sensitivity (at 95% specificity) of 61%; AGP, NGAL, and A2M sensitivity was 51-52%. AUC for albumin was 0.72 with sensitivity of 39%. A2M was the best performer in studies with only SIR (AUC 0.91). In the subset of studies with drug-induced vascular injury, TIMP-1 performed best with an AUC of 0.96. Poor performance of all tested biomarkers was observed in samples with CNS toxicity. In summary, TIMP-1, A2M, AGP and NGAL demonstrated performance as sensitive accessible biomarkers of DITI and SIR, supporting their potential application as universal accessible tissue toxicity biomarkers to quickly identify dose levels associated with drug-induced injury in early exploratory rat safety and other studies.
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Gu YZ, Handt L, Vlasakova K, Bakthavatchalu V, Smith R, Fernandez GE, Born SL, Glaab WE, Sistare FD. Kidney Injury Monitoring in Tobramycin-Treated Rhesus Monkeys: Supplementing Urinary Kidney Biomarkers With Kidney Biopsy Gene Expression Profiling. Toxicol Pathol 2021; 50:35-46. [PMID: 34657537 DOI: 10.1177/01926233211049171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Kidney biopsies are used sparingly to diagnose kidney injury in the clinic. Here we have conducted a small exploratory study to directly compare the low-grade kidney injury monitoring performance of serum safety biomarkers, novel urine safety biomarkers, microscopic histopathology and targeted gene expression alterations in kidney biopsy specimens in rhesus monkeys treated with tobramycin. Targeted gene expression increases were observed in the kidney biopsy samples and whole kidney sections for kidney injury molecule 1 (KIM-1), clusterin (CLU), osteopontin (OPN) messenger RNA transcripts. In addition, increases of the urinary kidney safety protein biomarkers including KIM-1, CLU, OPN were also observed. These increases in gene expression and urinary protein end point were in concordance with the eventual low-grade kidney lesions seen in terminal tissue sections. In contrast, conventional serum biomarkers blood urea nitrogen and serum creatinine were not as sensitive in monitoring kidney injury. Although these data do not support routinely adding kidney biopsies to regular toxicology studies, they provide evidence on the value and limitations of incorporating gene expression profiling on kidney biopsy specimens, further underscore the value of urinary kidney safety biomarkers for improved low-grade kidney injury monitoring, and open the door for future definitive studies.
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Affiliation(s)
- Yi-Zhong Gu
- Safety Assessment and Laboratory Animal Resources, 2793Merck & Co, Inc, West Point, PA, USA
| | - Larry Handt
- Safety Assessment and Laboratory Animal Resources, 2793Merck & Co, Inc, West Point, PA, USA
| | - Katerina Vlasakova
- Safety Assessment and Laboratory Animal Resources, 2793Merck & Co, Inc, West Point, PA, USA
| | | | - Roger Smith
- Safety Assessment and Laboratory Animal Resources, 2793Merck & Co, Inc, West Point, PA, USA
| | - Guillermo E Fernandez
- Safety Assessment and Laboratory Animal Resources, 2793Merck & Co, Inc, West Point, PA, USA
| | - Stephanie L Born
- Safety Assessment and Laboratory Animal Resources, 2793Merck & Co, Inc, West Point, PA, USA
| | - Warren E Glaab
- Safety Assessment and Laboratory Animal Resources, 2793Merck & Co, Inc, West Point, PA, USA
| | - Frank D Sistare
- Safety Assessment and Laboratory Animal Resources, 2793Merck & Co, Inc, West Point, PA, USA
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