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Ferreira RM, de Almeida R, Culp C, Witzmann F, Wang M, Kher R, Nagami GT, Mohallem R, Andolino CJ, Aryal UK, Eadon MT, Bacallao RL. Proteomic analysis of murine kidney proximal tubule sub-segment derived cell lines reveals preferences in mitochondrial pathway activity. J Proteomics 2023; 289:104998. [PMID: 37657718 PMCID: PMC10843797 DOI: 10.1016/j.jprot.2023.104998] [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: 04/19/2023] [Revised: 07/16/2023] [Accepted: 08/28/2023] [Indexed: 09/03/2023]
Abstract
The proximal tubule (PT) is a nephron segment that is responsible for the majority of solute and water reabsorption in the kidney. Each of its sub-segments have specialized functions; however, little is known about the genes and proteins that determine the oxidative phosphorylation capacity of the PT sub-segments. This information is critical to understanding kidney function and will provide a comprehensive landscape of renal cell adaptations to injury, physiologic stressors, and development. This study analyzed three immortalized murine renal cell lines (PT S1, S2, and S3 segments) for protein content and compared them to a murine fibroblast cell line. All three proximal tubule cell lines generate ATP predominantly by oxidative phosphorylation while the fibroblast cell line is glycolytic. The proteomic data demonstrates that the most significant difference in proteomic signatures between the cell lines are proteins known to be localized in the nucleus followed by mitochondrial proteins. Mitochondrial metabolic substrate utilization assays were performed using the proximal tubule cell lines to determine substrate utilization kinetics thereby providing a physiologic context to the proteomic dataset. This data will allow researchers to study differences in nephron-specific cell lines, between epithelial and fibroblast cells, and between actively respiring cells and glycolytic cells. SIGNIFICANCE: Proteomic analysis of proteins expressed in immortalized murine renal proximal tubule cells was compared to a murine fibroblast cell line proteome. The proximal tubule segment specific cell lines: S1, S2 and S3 are all grown under conditions whereby the cells generate ATP by oxidative phosphorylation while the fibroblast cell line utilizes anaerobic glycolysis for ATP generation. The proteomic studies allow for the following queries: 1) comparisons between the proximal tubule segment specific cell lines, 2) comparisons between polarized epithelia and fibroblasts, 3) comparison between cells employing oxidative phosphorylation versus anaerobic glycolysis and 4) comparisons between cells grown on clear versus opaque membrane supports. The data finds major differences in nuclear protein expression and mitochondrial proteins. This proteomic data set will be an important baseline dataset for investigators who need immortalized renal proximal tubule epithelial cells for their research.
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Affiliation(s)
- Ricardo Melo Ferreira
- Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
| | - Rita de Almeida
- Instituto de Física and Instituto Nacional de Ciência e Tecnologia, Universidade Federal do Rio Grande do Sul, 91501-970 Porto Alegre, RS, Brazil.
| | - Clayton Culp
- Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
| | - Frank Witzmann
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
| | - Mu Wang
- Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
| | - Rajesh Kher
- Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
| | - Glenn T Nagami
- Division of Nephrology, VA Greater Los Angeles Healthcare System, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
| | - Rodrigo Mohallem
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA; Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA.
| | - Chaylen Jade Andolino
- Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA.
| | - Uma K Aryal
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA; Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA.
| | - Michael T Eadon
- Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
| | - Robert L Bacallao
- Division of Nephrology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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de Kok MJC, Schaapherder AF, Wüst RCI, Zuiderwijk M, Bakker JA, Lindeman JHN, Le Dévédec SE. Circumventing the Crabtree effect in cell culture: A systematic review. Mitochondrion 2021; 59:83-95. [PMID: 33812964 DOI: 10.1016/j.mito.2021.03.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/08/2021] [Accepted: 03/29/2021] [Indexed: 10/21/2022]
Abstract
Metabolic reprogramming and mitochondrial dysfunction are central elements in a broad variety of physiological and pathological processes. While cell culture established itself as a versatile technique for the elaboration of physiology and disease, studying metabolism using standard cell culture protocols is profoundly interfered by the Crabtree effect. This phenomenon refers to the adaptation of cultured cells to a glycolytic phenotype, away from oxidative phosphorylation in glucose-containing medium, and questions the applicability of cell culture in certain fields of research. In this systematic review we aim to provide a comprehensive overview and critical appraisal of strategies reported to circumvent the Crabtree effect.
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Affiliation(s)
- Michèle J C de Kok
- Department of Surgery and Leiden Transplant Center, Leiden University Medical Center, Leiden, The Netherlands
| | - Alexander F Schaapherder
- Department of Surgery and Leiden Transplant Center, Leiden University Medical Center, Leiden, The Netherlands
| | - Rob C I Wüst
- Laboratory for Myology, Faculty of Behavioural and Movement Sciences, Amsterdam Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Melissa Zuiderwijk
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Jaap A Bakker
- Department of Clinical Chemistry & Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Jan H N Lindeman
- Department of Surgery and Leiden Transplant Center, Leiden University Medical Center, Leiden, The Netherlands
| | - Sylvia E Le Dévédec
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands.
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Mitochondrial glutathione transport: physiological, pathological and toxicological implications. Chem Biol Interact 2006; 163:54-67. [PMID: 16600197 DOI: 10.1016/j.cbi.2006.03.001] [Citation(s) in RCA: 204] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2006] [Revised: 02/28/2006] [Accepted: 03/01/2006] [Indexed: 01/05/2023]
Abstract
Although most cellular glutathione (GSH) is in the cytoplasm, a distinctly regulated pool is present in mitochondria. Inasmuch as GSH synthesis is primarily restricted to the cytoplasm, the mitochondrial pool must derive from transport of cytoplasmic GSH across the mitochondrial inner membrane. Early studies in liver mitochondria primarily focused on the relationship between GSH status and membrane permeability and energetics. Because GSH is an anion at physiological pH, this suggested that some of the organic anion carriers present in the inner membrane could function in GSH transport. Indeed, studies by Lash and colleagues in isolated mitochondria from rat kidney showed that most of the transport (>80%) in that tissue could be accounted for by function of the dicarboxylate carrier (DIC, Slc25a10) and the oxoglutarate carrier (OGC, Slc25a11), which mediate electroneutral exchange of dicarboxylates for inorganic phosphate and 2-oxoglutarate for other dicarboxylates, respectively. The identity and function of specific carrier proteins in other tissues is less certain, although the OGC is expressed in heart, liver, and brain and the DIC is expressed in liver and kidney. An additional carrier that transports 2-oxoglutarate, the oxodicarboxylate or oxoadipate carrier (ODC; Slc25a21), has been described in rat and human liver and its expression has a wide tissue distribution, although its potential function in GSH transport has not been investigated. Overexpression of the cDNA for the DIC and OGC in a renal proximal tubule-derived cell line, NRK-52E cells, showed that enhanced carrier expression and activity protects against oxidative stress and chemically induced apoptosis. This has implications for development of novel therapeutic approaches for treatment of human diseases and pathological states. Several conditions, such as alcoholic liver disease, cirrhosis or other chronic biliary obstructive diseases, and diabetic nephropathy, are associated with depletion or oxidation of the mitochondrial GSH pool in liver or kidney.
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Genestie I, Morin JP, Guery C, Bode G, Lorenzon G. Morphological and biochemical characterization of primary culture of rabbit proximal kidney tubule cells grown on collagen-IV coated Millicell-CM. In Vitro Cell Dev Biol Anim 1997; 33:692-702. [PMID: 9358285 DOI: 10.1007/s11626-997-0127-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The aim of this study was to better characterize rabbit proximal kidney tubule cells cultured on collagen IV-coated porous inserts, as compared to the same cells seeded in standard plastic wells. Total protein contents in confluent monolayers on permeable membranes were about twofold higher than those measured in confluent cultures in plastic wells. Microscopy examinations suggested that such a difference was probably due to a higher cell density and to an impressive development of the apical brush-border membrane. Moreover, measurement of unidirectional transport of p-aminohippuric acid and tetraethylammonium bromide confirmed the high polarization level of cultures on porous inserts. Results of methyl(alpha-D-[U-14C]glyco)pyranoside uptake suggested that cell phenotype was probably influenced by culture conditions. Analysis of different markers as a function of time in culture showed decreases of alkaline phosphatase (AP), gamma-glutamyltranspeptidase (GGT), and Na(+)-K(+)-ATPase activities as well as increases in LDH, ATP, and glutathione levels, similar to those formerly reported for cells cultured in standard plastic plates. However, comparative data from 6-d-old monolayers have shown that AP, GGT, Na(+)-K(+)-ATPase, glutathione reductase (GRED), and selenium-dependent glutathione peroxidase (Se-GPX) activities were 2.8-, 2.6-, 1.6-, 1.2-, and 2.1-fold, respectively, better preserved on precoated permeable membranes. On the other hand, this paper reports for the first time in the literature that GRED and SE-GPX, two phase II detoxification enzymes, were well maintained in cultures of rabbit proximal kidney tubule cells. Our results show that culturing rabbit proximal kidney tubule cells on collagen IV-coated porous membranes was accompanied by an improvement of both morphological and biochemical properties of the cells.
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Affiliation(s)
- I Genestie
- Département de Toxicologie, Roussel Uclaf, Romainville, France
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Nowak G, Schnellmann RG. L-ascorbic acid regulates growth and metabolism of renal cells: improvements in cell culture. THE AMERICAN JOURNAL OF PHYSIOLOGY 1996; 271:C2072-80. [PMID: 8997210 DOI: 10.1152/ajpcell.1996.271.6.c2072] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The addition of L-ascorbic acid 2-phosphate (AscP) to primary cultures of rabbit renal proximal tubular cells (RPTC) grown under improved culture conditions resulted in an extended growth phase and increased cellular density (1.3-fold increase in monolayer DNA and protein contents). AscP reduced glycolysis, increased net lactate consumption by 38%, and stimulated net glucose production by 47%. Basal O2 consumption increased by 39% in RPTC grown in the presence of AscP and was equivalent to that in freshly isolated proximal tubules. AscP increased ouabain-sensitive O2 consumption (81%) and Na(+)-K(+)-ATPase activity (2.5-fold), which suggested increased active Na+ transport. Addition of AscP increased Na(+)-dependent glucose uptake by 43% and brush-border enzyme marker activities by 46%. It is concluded that supplementation of media with AscP further improves RPTC culture conditions by promotion of cellular growth and stimulation of in vivo-like respiration, lactate utilization, and net glucose synthesis. These changes are accompanied by an increase in brush-border enzyme activities and stimulation of active Na+ transport and Na(+)-dependent glucose transport, which demonstrate an improved expression of brush-border membrane functions in RPTC.
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Affiliation(s)
- G Nowak
- Department of Pharmacology and Toxicology, University of Arkansas for Medical Sciences, Little Rock 72205-7199, USA
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Nowak G, Schnellmann RG. Improved culture conditions stimulate gluconeogenesis in primary cultures of renal proximal tubule cells. THE AMERICAN JOURNAL OF PHYSIOLOGY 1995; 268:C1053-61. [PMID: 7733227 DOI: 10.1152/ajpcell.1995.268.4.c1053] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Unlike renal proximal tubule cells (RPTC) in vivo, RPTC cultured in standard conditions are hypoxic, glycolytic, and not gluconeogenic. This study investigated the effects of glucose and lactate on glycolysis and gluconeogenesis in rabbit RPTC cultured in conditions of increased oxygen supply (Shake). Confluent Shake cultures grown in the presence of glucose exhibited increased oxygen consumption and decreased glycolysis compared with stationary (Still) cultures. Addition of 5 mM lactate to a 5 mM glucose medium decreased net glucose consumption and glucose oxidation in Shake cultures by 34 and 50%, respectively, and resulted in net lactate consumption. Addition of 5 mM lactate to a glucose-free medium resulted in a threefold increase in net glucose production (0.024 +/- 0.003 vs. 0.074 +/- 0.013 mumol.mg protein-1.day-1) in Shake cultures. Net glucose production further increased to 0.430 +/- 0.020 and 1.640 +/- 0.040 mumol.mg protein-1.day-1 when glucose reuptake was inhibited by 1 mM phloridzin or 1 mM phloridzin + 1 mM phloretin, respectively. These results show that, under conditions of improved oxygenation and in the presence of lactate and physiological levels of glucose and insulin, RPTC aerobic metabolism increases and glucose metabolism changes from glycolysis and net lactate production to gluconeogenesis and net lactate consumption.
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Affiliation(s)
- G Nowak
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens 30602-7389, USA
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Griner RD, Schnellmann RG. Decreasing glycolysis increases sensitivity to mitochondrial inhibition in primary cultures of renal proximal tubule cells. In Vitro Cell Dev Biol Anim 1994; 30A:30-4. [PMID: 8193771 DOI: 10.1007/bf02631415] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We have previously shown that shaking the culture plates (SHAKE) of rabbit renal proximal tubule cells (RPTC) to maintain adequate aeration increased aerobic metabolism and decreased the induction of glycolysis compared to RPTC cultured under standard conditions (STILL). However, glycolysis in SHAKE RPTC remained elevated compared to glycolysis in proximal tubules in vivo. In the present study the contribution of culture medium sugar composition and concentration to glycolytic metabolism was assessed in RPTC. SHAKE and STILL RPTC cultured in 5 mM glucose contained lactate levels equivalent to the respective SHAKE and STILL RPTC cultured in standard culture medium which contains 17.5 mM glucose. Similarly, the activity of lactate dehydrogenase was unchanged by lowering the medium glucose concentration. Substituting 5 mM galactose for 5 mM glucose in the culture medium significantly reduced the lactate content of both SHAKE and STILL RPTC but had no effect on lactate dehydrogenase activity. Cell growth was equivalent under all culture conditions. Sensitivity to mitochondrial inhibition was determined for each culture condition by measuring cell death after exposure to the respiratory inhibitor antimycin A. The results showed a hierarchy of sensitivity to antimycin A (5 mM galactose SHAKE > 5 mM glucose SHAKE > 17.5 mM glucose SHAKE = 17.5 mM glucose STILL), which was generally inversely correlated with the level of glycolysis as measured by lactate content (17.5 mM glucose STILL > 17.5 mM glucose SHAKE = 5 mM glucose SHAKE > 5 mM galactose SHAKE).
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Affiliation(s)
- R D Griner
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens 30602
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