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Douchant K, He SM, Noordhof C, Greenlaw J, Vancuren S, Schroeter K, Allen-Vercoe E, Sjaarda C, Vanner SJ, Petrof EO, Sheth PM, Guzman M. Defined microbial communities and their soluble products protect mice from Clostridioides difficile infection. Commun Biol 2024; 7:135. [PMID: 38280981 PMCID: PMC10821944 DOI: 10.1038/s42003-024-05778-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 01/03/2024] [Indexed: 01/29/2024] Open
Abstract
Clostridioides difficile is the leading cause of antibiotic-associated infectious diarrhea. The development of C.difficile infection is tied to perturbations of the bacterial community in the gastrointestinal tract, called the gastrointestinal microbiota. Repairing the gastrointestinal microbiota by introducing lab-designed bacterial communities, or defined microbial communities, has recently shown promise as therapeutics against C.difficile infection, however, the mechanisms of action of defined microbial communities remain unclear. Using an antibiotic- C.difficile mouse model, we report the ability of an 18-member community and a refined 4-member community to protect mice from two ribotypes of C.difficile (CD027, CD078; p < 0.05). Furthermore, bacteria-free supernatant delivered orally to mice from the 4-member community proteolyzed C.difficile toxins in vitro and protected mice from C.difficile infection in vivo (p < 0.05). This study demonstrates that bacteria-free supernatant is sufficient to protect mice from C.difficile; and could be further explored as a therapeutic strategy against C.difficile infection.
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Affiliation(s)
- Katya Douchant
- The Gastrointestinal Disease Research Unit (GIDRU), Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, K7L3N6, ON, Canada
| | - Shu-Mei He
- The Gastrointestinal Disease Research Unit (GIDRU), Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada
| | - Curtis Noordhof
- The Gastrointestinal Disease Research Unit (GIDRU), Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada
| | - Jill Greenlaw
- The Gastrointestinal Disease Research Unit (GIDRU), Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada
| | - Sarah Vancuren
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G2W1, ON, Canada
| | - Kathleen Schroeter
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G2W1, ON, Canada
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G2W1, ON, Canada
| | - Calvin Sjaarda
- The Gastrointestinal Disease Research Unit (GIDRU), Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, K7L3N6, ON, Canada
- Division of Microbiology, Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada
| | - Stephen J Vanner
- The Gastrointestinal Disease Research Unit (GIDRU), Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, K7L3N6, ON, Canada
| | - Elaine O Petrof
- The Gastrointestinal Disease Research Unit (GIDRU), Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada
| | - Prameet M Sheth
- The Gastrointestinal Disease Research Unit (GIDRU), Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada.
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, K7L3N6, ON, Canada.
- Division of Microbiology, Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada.
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, K7L3N6, ON, Canada.
| | - Mabel Guzman
- The Gastrointestinal Disease Research Unit (GIDRU), Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada
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Al-Qazazi R, Emon IM, Potus F, Martin AY, Lima PDA, Vlasschaert C, Chen KH, Wu D, Gupta AD, Noordhof C, Jefferson L, McNaughton AJM, Bick AG, Pauciulo MW, Nichols WC, Chung WK, Hassoun PM, Damico RL, Rauh MJ, Archer SL. Germline and Somatic Mutations in DNA Methyltransferase 3A (DNMT3A) Predispose to Pulmonary Arterial Hypertension (PAH) in Humans and Mice: Implications for Associated PAH. medRxiv 2023:2023.12.30.23300391. [PMID: 38234783 PMCID: PMC10793539 DOI: 10.1101/2023.12.30.23300391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Background Mutations are found in 10-20% of idiopathic PAH (IPAH) patients, but none are consistently identified in connective tissue disease-associated PAH (APAH), which accounts for ∼45% of PAH cases. TET2 mutations, a cause of clonal hematopoiesis of indeterminant potential (CHIP), predispose to an inflammatory type of PAH. We now examine mutations in another CHIP gene, DNMT3A , in PAH. Methods We assessed DNMT3A mutation prevalence in PAH Biobank subjects as compared with controls, first using whole exome sequencing (WES)-derived CHIP calls in 1832 PAH Biobank patients versus 7509 age-and sex-matched gnomAD controls. We then performed deep, targeted panel sequencing of CHIP genes on a subset of 710 PAH Biobank patients and compared the prevalence of DNMT3A mutations therein to an independent pooled control cohort (N = 3645). In another cohort of 80 PAH patients and 41 controls, DNMT3A mRNA expression was studied in peripheral blood mononuclear cells (PBMCs). Finally, we evaluated the development of PAH in a conditional, hematopoietic, Dnmt3a knockout mouse model. Results DNMT3A mutations were more frequent in PAH cases versus control subjects in the WES dataset (OR 2.60, 95% CI: 1.71-4.27). Among PAH patients, 33 had DNMT3A variants, most of whom had APAH (21/33). While 21/33 had somatic mutations (female:male 17:4), germline variants occurred in 12/33 (female:male 11:1). Hemodynamics were comparable with and without DNMT3A mutations (mPAP=58±21 vs. 52±18 mmHg); however, patients with DNMT3A mutations were unresponsive to acute vasodilator testing. Targeted panel sequencing identified that 14.6% of PAH patients had CHIP mutations (104/710), with DNMT3A accounting for 49/104. There was a significant association between all CHIP mutations and PAH in analyses adjusted for age and sex (OR 1.40, 95% CI: 1.09-1.80), though DNMT3A CHIP alone was not significantly enriched (OR:1.15, 0.82-1.61). DNMT3A expression was reduced in patient-derived versus control PAH-PBMCs. Spontaneous PAH developed in Dnmt3a -/- mice, and it was exacerbated by 3 weeks of hypoxia. Dnmt3a -/- mice had increased lung macrophages and elevated plasma IL-13. The IL-1β antibody canakinumab attenuated PAH in Dnmt3a -/- mice. Conclusions Germline and acquired DNMT3A variants predispose to PAH in humans. DNMT3A mRNA expression is reduced in human PAH PBMCs. Hematopoietic depletion of Dnmt3a causes inflammatory PAH in mice. DNMT3A is a novel APAH gene and may be a biomarker and therapeutic target.
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Roberge N, Neville N, Douchant K, Noordhof C, Boev N, Sjaarda C, Sheth PM, Jia Z. Broad-Spectrum Inhibitor of Bacterial Polyphosphate Homeostasis Attenuates Virulence Factors and Helps Reveal Novel Physiology of Klebsiella pneumoniae and Acinetobacter baumannii. Front Microbiol 2021; 12:764733. [PMID: 34764949 PMCID: PMC8576328 DOI: 10.3389/fmicb.2021.764733] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/04/2021] [Indexed: 12/26/2022] Open
Abstract
Acinetobacter baumannii and Klebsiella pneumoniae currently rank amongst the most antibiotic-resistant pathogens, responsible for millions of infections each year. In the wake of this crisis, anti-virulence therapeutics targeting bacterial polyphosphate (polyP) homeostasis have been lauded as an attractive alternative to traditional antibiotics. In this work, we show that the small molecule gallein, a known G-protein βγ subunit modulator, also recently proven to have dual-specificity polyphosphate kinase (PPK) inhibition in Pseudomonas aeruginosa, in turn exhibits broad-spectrum PPK inhibition in other priority pathogens. Gallein treatment successfully attenuated virulence factors of K. pneumoniae and A. baumannii including biofilm formation, surface associated motility, and offered protection against A. baumannii challenge in a Caenorhabditis elegans model of infection. This was highlighted most importantly in the critically understudied A. baumannii, where gallein treatment phenocopied a ppk1 knockout strain of a previously uncharacterized PPK1. Subsequent analysis revealed a unique instance of two functionally and phenotypically distinct PPK1 isoforms encoded by a single bacterium. Finally, gallein was administered to a defined microbial community comprising over 30 commensal species of the human gut microbiome, demonstrating the non-disruptive properties characteristic of anti-virulence treatments as microbial biodiversity was not adversely influenced. Together, these results emphasize that gallein is a promising avenue for the development of broad-spectrum anti-virulence therapeutics.
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Affiliation(s)
- Nathan Roberge
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Nolan Neville
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Katya Douchant
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada.,Gastrointestinal Disease Research Unit (GIDRU), Department of Medicine, Queen's University, Kingston, ON, Canada
| | - Curtis Noordhof
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada.,Gastrointestinal Disease Research Unit (GIDRU), Department of Medicine, Queen's University, Kingston, ON, Canada
| | - Nadejda Boev
- Queen's Genomics Lab at Ongwanada (Q-GLO), Ongwanada Resource Center, Kingston, ON, Canada
| | - Calvin Sjaarda
- Queen's Genomics Lab at Ongwanada (Q-GLO), Ongwanada Resource Center, Kingston, ON, Canada.,Department of Psychiatry, Queen's University, Kingston, ON, Canada
| | - Prameet M Sheth
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada.,Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada.,Gastrointestinal Disease Research Unit (GIDRU), Department of Medicine, Queen's University, Kingston, ON, Canada.,Division of Microbiology, Kingston Health Science Center, Kingston, ON, Canada
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
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Martz SL, Guzman-Rodriguez M, He SM, Noordhof C, Hurlbut DJ, Gloor GB, Carlucci C, Weese S, Allen-Vercoe E, Sun J, Claud EC, Petrof EO. A human gut ecosystem protects against C. difficile disease by targeting TcdA. J Gastroenterol 2017; 52:452-465. [PMID: 27329502 PMCID: PMC5177537 DOI: 10.1007/s00535-016-1232-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 06/06/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND A defined Microbial Ecosystem Therapeutic (MET-1, or "RePOOPulate") derived from the feces of a healthy volunteer can cure recurrent C. difficile infection (rCDI) in humans. The mechanisms of action whereby healthy microbiota protect against rCDI remain unclear. Since C. difficile toxins are largely responsible for the disease pathology of CDI, we hypothesized that MET-1 exerts its protective effects by inhibiting the effects of these toxins on the host. METHODS A combination of in vivo (antibiotic-associated mouse model of C. difficile colitis, mouse ileal loop model) and in vitro models (FITC-phalloidin staining, F actin Western blots and apoptosis assay in Caco2 cells, transepithelial electrical resistance measurements in T84 cells) were employed. RESULTS MET-1 decreased both local and systemic inflammation in infection and decreased both the cytotoxicity and the amount of TcdA detected in stool, without an effect on C. difficile viability. MET-1 protected against TcdA-mediated damage in a murine ileal loop model. MET-1 protected the integrity of the cytoskeleton in cells treated with purified TcdA, as indicated by FITC-phalloidin staining, F:G actin assays and preservation of transepithelial electrical resistance. Finally, co-incubation of MET-1 with purified TcdA resulted in decreased detectable TcdA by Western blot analysis. CONCLUSIONS MET-1 intestinal microbiota confers protection against C. difficile and decreases C. difficile-mediated inflammation through its protective effects against C. difficile toxins, including enhancement of host barrier function and degradation of TcdA. The effect of MET-1 on C. difficile viability seems to offer little, if any, contribution to its protective effects on the host.
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Affiliation(s)
- Sarah Lynn Martz
- Division of Infectious Diseases/GI Diseases Research Unit Wing, Department of Medicine, Kingston General Hospital, Queen's University, 76 Stuart Street, Kingston, ON, K7L 2V7, Canada
| | - Mabel Guzman-Rodriguez
- Division of Infectious Diseases/GI Diseases Research Unit Wing, Department of Medicine, Kingston General Hospital, Queen's University, 76 Stuart Street, Kingston, ON, K7L 2V7, Canada
| | - Shu-Mei He
- Division of Infectious Diseases/GI Diseases Research Unit Wing, Department of Medicine, Kingston General Hospital, Queen's University, 76 Stuart Street, Kingston, ON, K7L 2V7, Canada
| | - Curtis Noordhof
- Division of Infectious Diseases/GI Diseases Research Unit Wing, Department of Medicine, Kingston General Hospital, Queen's University, 76 Stuart Street, Kingston, ON, K7L 2V7, Canada
| | - David John Hurlbut
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, K7L 2V7, Canada
| | - Gregory Brian Gloor
- Department of Biochemistry, University of Western Ontario, London, ON, N6A 5C1, Canada
| | - Christian Carlucci
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Scott Weese
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Jun Sun
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Erika Chiong Claud
- Departments of Pediatrics and Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Elaine Olga Petrof
- Division of Infectious Diseases/GI Diseases Research Unit Wing, Department of Medicine, Kingston General Hospital, Queen's University, 76 Stuart Street, Kingston, ON, K7L 2V7, Canada.
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Abstract
Using a murine Salmonella model of colitis, we recently reported that mice receiving a community of defined gut microbiota (MET-1) lost less weight, had reduced systemic inflammation and splenic S. typhimurium infection, and decreased neutrophil infiltration in the cecum, compared to vehicle controls. In addition, animals receiving MET-1 exhibited preserved tight junction protein expression (Zonula occludens-1, claudin-1), suggesting important effects on barrier function. In this addendum, we describe additional in vitro experiments examining effects of MET-1, as well as in vivo experiments demonstrating that MET-1 is protective in a DSS model of colitis after administration of antibiotics. Placed in the context of our findings and those of others, we discuss differences in our findings between the Salmonella colitis and DSS colitis models, provide speculation as to which bacteria may be important in the protective effects of MET-1, and discuss potential implications for other GI diseases such as IBD.
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Affiliation(s)
- Sean Munoz
- Department of Medicine, Division of Infectious Diseases/GI Diseases Research Unit, Queen's University, Kingston, ON, Canada
| | - Mabel Guzman-Rodriguez
- Department of Medicine, Division of Infectious Diseases/GI Diseases Research Unit, Queen's University, Kingston, ON, Canada
| | - Jun Sun
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL, USA
| | - Yong-guo Zhang
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL, USA
| | - Curtis Noordhof
- Department of Medicine, Division of Infectious Diseases/GI Diseases Research Unit, Queen's University, Kingston, ON, Canada
| | - Shu-Mei He
- Department of Medicine, Division of Infectious Diseases/GI Diseases Research Unit, Queen's University, Kingston, ON, Canada
| | - Emma Allen-Vercoe
- Department of Molecular & Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Erika C. Claud
- Department of Pediatrics and Medicine, University of Chicago, Chicago, IL, USA
| | - Elaine O. Petrof
- Department of Medicine, Division of Infectious Diseases/GI Diseases Research Unit, Queen's University, Kingston, ON, Canada
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Luke MM, Kane JP, Liu DM, Rowland CM, Shiffman D, Cassano J, Catanese JJ, Pullinger CR, Leong DU, Arellano AR, Tong CH, Movsesyan I, Naya-Vigne J, Noordhof C, Feric NT, Malloy MJ, Topol EJ, Koschinsky ML, Devlin JJ, Ellis SG. A polymorphism in the protease-like domain of apolipoprotein(a) is associated with severe coronary artery disease. Arterioscler Thromb Vasc Biol 2007; 27:2030-6. [PMID: 17569884 DOI: 10.1161/atvbaha.107.141291] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVES The purpose of this study was to identify genetic variants associated with severe coronary artery disease (CAD). METHODS AND RESULTS We used 3 case-control studies of white subjects whose severity of CAD was assessed by angiography. The first 2 studies were used to generate hypotheses that were then tested in the third study. We tested 12,077 putative functional single nucleotide polymorphisms (SNPs) in Study 1 (781 cases, 603 controls) and identified 302 SNPs nominally associated with severe CAD. Testing these 302 SNPs in Study 2 (471 cases, 298 controls), we found 5 (in LPA, CALM1, HAP1, AP3B1, and ABCG2) were nominally associated with severe CAD and had the same risk alleles in both studies. We then tested these 5 SNPs in Study 3 (554 cases, 373 controls). We found 1 SNP that was associated with severe CAD: LPA I4399M (rs3798220). LPA encodes apolipoprotein(a), a component of lipoprotein(a). I4399M is located in the protease-like domain of apolipoprotein(a). Compared with noncarriers, carriers of the 4399M risk allele (2.7% of controls) had an adjusted odds ratio for severe CAD of 3.14 (confidence interval 1.51 to 6.56), and had 5-fold higher median plasma lipoprotein(a) levels (P=0.003). CONCLUSIONS The LPA I4399M SNP is associated with severe CAD and plasma lipoprotein(a) levels.
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Affiliation(s)
- May M Luke
- Celera, 1401 Harbor Bay Parkway, Alameda, CA 94502, USA.
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Pilkey RM, Morton AR, Boffa MB, Noordhof C, Day AG, Su Y, Miller LM, Koschinsky ML, Booth SL. Subclinical vitamin K deficiency in hemodialysis patients. Am J Kidney Dis 2007; 49:432-9. [PMID: 17336705 DOI: 10.1053/j.ajkd.2006.11.041] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2006] [Accepted: 11/22/2006] [Indexed: 11/11/2022]
Abstract
BACKGROUND Subclinical vitamin K deficiency increasingly is associated with extraosseous calcification in healthy adults. Nondietary determinants of vitamin K status include apolipoprotein E (apoE) genotype, which may influence vitamin K transport to peripheral tissues. METHODS Serum phylloquinone concentrations and percentage of uncarboxyated osteocalcin (%ucOC) were measured by means of high-performance liquid chromatography and radioimmunoassay in 142 hemodialysis patients, respectively. ApoE phenotype was determined by means of isoelectric focusing of delipidated serum samples and Western blot analysis. Clinical and laboratory data were obtained by using chart review. RESULTS Mean age was 62.6 +/- 14.8 (SD) years. Mean phylloquinone level was 0.99 +/- 1.12 nmol/L; 29% of patients had levels less than 0.4 nmol/L. There was no association between phylloquinone level and %ucOC. There were positive correlations between phylloquinone and total cholesterol (P = 0.017), triglyceride (P = 0.022), and ionized calcium levels (P = 0.019). There was a negative correlation between phylloquinone level and dialysis adequacy (P = 0.002). Mean %ucOC was 51.1% +/- 25.8%, and 93% of subjects had values greater than 20%. There were positive correlations between %ucOC and dialysis vintage (P < 0.001), phosphate level (P < 0.001), parathyroid hormone level (P < 0.001), albumin level (P = 0.035), and ionized calcium level (P = 0.046). Seventeen percent of patients were apoE4. Mean %ucOC was significantly greater in apoE4 carriers compared with all other apoE phenotypes (60.1% +/- 28.4% versus 47.8% +/- 24.4%; P = 0.035). In multiple regression analysis with phylloquinone level forced in, independent predictors of %ucOC were phosphate level, dialysis vintage, parathyroid hormone level, and apoE4. CONCLUSION These data indicate suboptimal vitamin K status in hemodialysis patients, shown by low phylloquinone concentrations and high %ucOC in 29% and 93% of subjects, respectively. The apoE4 allele influences osteocalcin gamma-carboxylation in hemodialysis patients.
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Affiliation(s)
- Rachel M Pilkey
- Division of Nephrology, Queen's University, Kingston, Ontario, Canada.
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