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Van Dyck PK, Piszkin L, Gorski EA, Nascimento ET, Abebe JA, Hoffmann LM, Peng JW, White KA. Ionizable networks mediate pH-dependent allostery in SH2 signaling proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.21.608875. [PMID: 39229188 PMCID: PMC11370553 DOI: 10.1101/2024.08.21.608875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Transient intracellular pH dynamics 1 regulate mammalian proliferation 2,3 , migration 4 , and differentiation 5 . However, for many pH-dependent cell processes, the molecular mediators are unknown 6 . Prior work identified histidine residues as molecular switches in pH-sensitive proteins, but how other ionizable residues contribute to pH-dependent protein allostery is understudied. Here, we develop an in silico computational pipeline to identify putative pH-sensitive proteins and their molecular mechanisms. We first apply this pipeline to SHP2, a known pH-sensitive signaling protein with an uncharacterized molecular mechanism. We show wild-type SHP2 phosphatase activity is pH-sensitive in vitro and in cells, and mutation of identified H116 and E252 to non-titratable alanine residues abolishes pH-sensitive function. We also show that c-Src is a previously unrecognized pH-dependent kinase, and mutation of the identified ionizable network again abolishes pH-sensitive activity. Constant pH molecular dynamics simulations support a conserved allosteric mechanism of pH-dependent binding of inhibitory SH2 domains to the functional catalytic domains of SHP2 and c-Src. We apply our computational pipeline across SH2 domain-containing signaling proteins and identify evolutionarily conserved putative pH-sensing networks. Our results reveal that pH is an allosteric regulator of SH2 domain-containing signaling proteins providing insight into normal pH-dependent cell biology and diseases where pHi is dysregulated, such as cancer.
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2
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Romero-Moreno R, Czowski BJ, Harris L, Kuehn JF, White KA. Intracellular pH differentially regulates transcription of metabolic and signaling pathways in normal epithelial cells. J Biol Chem 2024:107658. [PMID: 39128712 DOI: 10.1016/j.jbc.2024.107658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Accepted: 07/31/2024] [Indexed: 08/13/2024] Open
Abstract
Intracellular pH (pHi) dynamics regulate normal cell function, and dysregulated pHi dynamics is an emerging hallmark of cancer (constitutively increased pHi) and neurodegeneration (constitutively decreased pHi). However, the molecular mechanisms by which pHi dynamics regulate cell biology are poorly understood. Here, we discovered that altering pHi in normal human breast epithelial cells triggers global transcriptional changes. We identified 176 genes differentially regulated by pHi, with pHi-dependent genes clustering in signaling and glycolytic pathways. Using various normal epithelial cell models, we showed pH-dependent Notch1 expression, with increased protein abundance at high pHi. This resulted in pH-dependent downstream signaling, with increased Notch1 signaling at high pHi. We also found that high pHi increased the expression of glycolytic enzymes and regulators of pyruvate fate, including lactate dehydrogenase and pyruvate dehydrogenase kinase. These transcriptional changes were sufficient to alter lactate production, with high pHi shifting these normal epithelial cells toward a glycolytic metabolism and increasing lactate production. Thus, pHi dynamics transcriptionally regulate signaling and metabolic pathways in normal epithelial cells. Our data reveal new molecular regulators of pHi-dependent biology and a role for increased pHi in driving the acquisition of cancer-associated signaling and metabolic changes in normal human epithelial cells.
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Affiliation(s)
- Ricardo Romero-Moreno
- Harper Cancer Research Institute, South Bend. IN, 46617, USA; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Brandon J Czowski
- Harper Cancer Research Institute, South Bend. IN, 46617, USA; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Lindsey Harris
- Harper Cancer Research Institute, South Bend. IN, 46617, USA; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Jessamine F Kuehn
- Harper Cancer Research Institute, South Bend. IN, 46617, USA; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Katharine A White
- Harper Cancer Research Institute, South Bend. IN, 46617, USA; Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA.
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3
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Kisor KP, Ruiz DG, Jacobson MP, Barber DL. A role for pH dynamics regulating transcription factor DNA binding selectivity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595212. [PMID: 38826444 PMCID: PMC11142074 DOI: 10.1101/2024.05.21.595212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Intracellular pH (pHi) dynamics regulates diverse cell processes such as proliferation, dysplasia, and differentiation, often mediated by the protonation state of a functionally critical histidine residue in endogenous pH sensing proteins. How pHi dynamics can directly regulate gene expression and whether transcription factors can function as pH sensors has received limited attention. We tested the prediction that transcription factors with a histidine in their DNA binding domain (DBD) that forms hydrogen bonds with nucleotides can have pH-regulated activity, which is relevant to more than 85 transcription factors in distinct families, including FOX, KLF, SOX and MITF/Myc. Focusing on FOX family transcription factors, we used unbiased SELEX-seq to identify pH-dependent DNA binding motif preferences, then confirm pH-regulated binding affinities for FOXC2, FOXM1, and FOXN1 to a canonical FkhP DNA motif that are 2.5 to 7.5 greater at pH 7.0 compared with pH 7.5. For FOXC2, we also find greater activity for an FkhP motif at lower pHi in cells and that pH-regulated binding and activity are dependent on a conserved histidine (His122) in the DBD. RNA-seq with FOXC2 also reveals pH-dependent differences in enriched promoter motifs. Our findings identify pH-regulated transcription factor-DNA binding selectivity with relevance to how pHi dynamics can regulate gene expression for myriad cell behaviours.
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4
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Stock C. pH-regulated single cell migration. Pflugers Arch 2024; 476:639-658. [PMID: 38214759 PMCID: PMC11006768 DOI: 10.1007/s00424-024-02907-2] [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: 11/22/2023] [Revised: 12/21/2023] [Accepted: 01/02/2024] [Indexed: 01/13/2024]
Abstract
Over the last two decades, extra- and intracellular pH have emerged as fundamental regulators of cell motility. Fundamental physiological and pathological processes relying on appropriate cell migration, such as embryonic development, wound healing, and a proper immune defense on the one hand, and autoimmune diseases, metastatic cancer, and the progression of certain parasitic diseases on the other, depend on surrounding pH. In addition, migrating single cells create their own localized pH nanodomains at their surface and in the cytosol. By this means, the migrating cells locally modulate their adhesion to, and the re-arrangement and digestion of, the extracellular matrix. At the same time, the cytosolic nanodomains tune cytoskeletal dynamics along the direction of movement resulting in concerted lamellipodia protrusion and rear end retraction. Extracellular pH gradients as found in wounds, inflamed tissues, or the periphery of tumors stimulate directed cell migration, and long-term exposure to acidic conditions can engender a more migratory and invasive phenotype persisting for hours up to several generations of cells after they have left the acidic milieu. In the present review, the different variants of pH-dependent single cell migration are described. The underlying pH-dependent molecular mechanisms such as conformational changes of adhesion molecules, matrix protease activity, actin (de-)polymerization, and signaling events are explained, and molecular pH sensors stimulated by H+ signaling are presented.
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Affiliation(s)
- Christian Stock
- Department of Gastroenterology, Hepatology, Infectiology & Endocrinology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
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5
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Michl J, White B, Monterisi S, Bodmer WF, Swietach P. Phenotypic screen of sixty-eight colorectal cancer cell lines identifies CEACAM6 and CEACAM5 as markers of acid resistance. Proc Natl Acad Sci U S A 2024; 121:e2319055121. [PMID: 38502695 PMCID: PMC10990159 DOI: 10.1073/pnas.2319055121] [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: 10/31/2023] [Accepted: 02/13/2024] [Indexed: 03/21/2024] Open
Abstract
Elevated cancer metabolism releases lactic acid and CO2 into the under-perfused tumor microenvironment, resulting in extracellular acidosis. The surviving cancer cells must adapt to this selection pressure; thus, targeting tumor acidosis is a rational therapeutic strategy to manage tumor growth. However, none of the major approved treatments are based explicitly on disrupting acid handling, signaling, or adaptations, possibly because the distinction between acid-sensitive and acid-resistant phenotypes is not clear. Here, we report pH-related phenotypes of sixty-eight colorectal cancer (CRC) cell lines by measuring i) extracellular acidification as a readout of acid production by fermentative metabolism and ii) growth of cell biomass over a range of extracellular pH (pHe) levels as a measure of the acid sensitivity of proliferation. Based on these measurements, CRC cell lines were grouped along two dimensions as "acid-sensitive"/"acid-resistant" versus "low metabolic acid production"/"high metabolic acid production." Strikingly, acid resistance was associated with the expression of CEACAM6 and CEACAM5 genes coding for two related cell-adhesion molecules, and among pH-regulating genes, of CA12. CEACAM5/6 protein levels were strongly induced by acidity, with a further induction under hypoxia in a subset of CRC lines. Lack of CEACAM6 (but not of CEACAM5) reduced cell growth and their ability to differentiate. Finally, CEACAM6 levels were strongly increased in human colorectal cancers from stage II and III patients, compared to matched samples from adjacent normal tissues. Thus, CEACAM6 is a marker of acid-resistant clones in colorectal cancer and a potential motif for targeting therapies to acidic regions within the tumors.
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Affiliation(s)
- Johanna Michl
- Department of Physiology, Anatomy and Genetics, University of Oxford, OxfordOX1 3PT, United Kingdom
| | - Bobby White
- Department of Physiology, Anatomy and Genetics, University of Oxford, OxfordOX1 3PT, United Kingdom
| | - Stefania Monterisi
- Department of Physiology, Anatomy and Genetics, University of Oxford, OxfordOX1 3PT, United Kingdom
| | - Walter F. Bodmer
- Department of Oncology, University of Oxford, OxfordOX3 7DQ, United Kingdom
| | - Pawel Swietach
- Department of Physiology, Anatomy and Genetics, University of Oxford, OxfordOX1 3PT, United Kingdom
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6
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Worthan SB, McCarthy RDP, Delaleau M, Stikeleather R, Bratton BP, Boudvillain M, Behringer MG. Evolution of pH-sensitive transcription termination during adaptation to repeated long-term starvation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.01.582989. [PMID: 38464051 PMCID: PMC10925284 DOI: 10.1101/2024.03.01.582989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Fluctuating environments that consist of regular cycles of co-occurring stress are a common challenge faced by cellular populations. For a population to thrive in constantly changing conditions, an ability to coordinate a rapid cellular response is essential. Here, we identify a mutation conferring an arginine-to-histidine (Arg to His) substitution in the transcription terminator Rho. The rho R109H mutation frequently arose in E. coli populations experimentally evolved under repeated long-term starvation conditions, during which feast and famine result in drastic environmental pH fluctuations. Metagenomic sequencing revealed that populations containing the rho mutation also possess putative loss-of-function mutations in ydcI, which encodes a recently characterized transcription factor associated with pH homeostasis. Genetic reconstructions of these mutations show that the rho allele confers a plastic alkaline-induced reduction of Rho function that, when found in tandem with a ΔydcI allele, leads to intracellular alkalinization and genetic assimilation of Rho mutant function. We further identify Arg to His substitutions at analogous sites in rho alleles from species originating from fluctuating alkaline environments. Our results suggest that Arg to His substitutions in global regulators of gene expression can serve to rapidly coordinate complex responses through pH sensing and shed light on how cellular populations across the tree of life use environmental cues to coordinate rapid responses to complex, fluctuating environments.
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Affiliation(s)
- Sarah B Worthan
- Department of Biological Sciences, Vanderbilt University, Nashville, TN
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN
| | | | - Mildred Delaleau
- Centre de Biophysique Moléculaire, CNRS UPR4301, affiliated with Université d'Orléans, rue Charles Sadron, 45071 Orléans cedex 2, France
| | - Ryan Stikeleather
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ
| | - Benjamin P Bratton
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
| | - Marc Boudvillain
- Centre de Biophysique Moléculaire, CNRS UPR4301, affiliated with Université d'Orléans, rue Charles Sadron, 45071 Orléans cedex 2, France
| | - Megan G Behringer
- Department of Biological Sciences, Vanderbilt University, Nashville, TN
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, TN
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ
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7
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Tsai YL, Arias-Badia M, Kadlecek TA, Lwin YM, Srinath A, Shah NH, Wang ZE, Barber D, Kuriyan J, Fong L, Weiss A. TCR signaling promotes formation of an STS1-Cbl-b complex with pH-sensitive phosphatase activity that suppresses T cell function in acidic environments. Immunity 2023; 56:2682-2698.e9. [PMID: 38091950 PMCID: PMC10785950 DOI: 10.1016/j.immuni.2023.11.010] [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: 01/23/2023] [Revised: 08/11/2023] [Accepted: 11/14/2023] [Indexed: 12/18/2023]
Abstract
T cell responses are inhibited by acidic environments. T cell receptor (TCR)-induced protein phosphorylation is negatively regulated by dephosphorylation and/or ubiquitination, but the mechanisms underlying sensitivity to acidic environments are not fully understood. Here, we found that TCR stimulation induced a molecular complex of Cbl-b, an E3-ubiquitin ligase, with STS1, a pH-sensitive unconventional phosphatase. The induced interaction depended upon a proline motif in Cbl-b interacting with the STS1 SH3 domain. STS1 dephosphorylated Cbl-b interacting phosphoproteins. The deficiency of STS1 or Cbl-b diminished the sensitivity of T cell responses to the inhibitory effects of acid in an autocrine or paracrine manner in vitro or in vivo. Moreover, the deficiency of STS1 or Cbl-b promoted T cell proliferative and differentiation activities in vivo and inhibited tumor growth, prolonged survival, and improved T cell fitness in tumor models. Thus, a TCR-induced STS1-Cbl-b complex senses intra- or extra-cellular acidity and regulates T cell responses, presenting a potential therapeutic target for improving anti-tumor immunity.
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Affiliation(s)
- Yuan-Li Tsai
- Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Marcel Arias-Badia
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Theresa A Kadlecek
- Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yee May Lwin
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Aahir Srinath
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Neel H Shah
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Zhi-En Wang
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Diane Barber
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John Kuriyan
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Lawrence Fong
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Arthur Weiss
- Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
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8
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Liu Y, Reyes E, Castillo-Azofeifa D, Klein OD, Nystul T, Barber DL. Intracellular pH dynamics regulates intestinal stem cell lineage specification. Nat Commun 2023; 14:3745. [PMID: 37353491 PMCID: PMC10290085 DOI: 10.1038/s41467-023-39312-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 06/06/2023] [Indexed: 06/25/2023] Open
Abstract
Intracellular pH dynamics is increasingly recognized to regulate myriad cell behaviors. We report a finding that intracellular pH dynamics also regulates adult stem cell lineage specification. We identify an intracellular pH gradient in mouse small intestinal crypts, lowest in crypt stem cells and increasing along the crypt column. Disrupting this gradient by inhibiting H+ efflux by Na+/H+ exchanger 1 abolishes crypt budding and blocks differentiation of Paneth cells, which are rescued with exogenous WNT. Using single-cell RNA sequencing and lineage tracing we demonstrate that intracellular pH dynamics acts downstream of ATOH1, with increased pH promoting differentiation toward the secretory lineage. Our findings indicate that an increase in pH is required for the lineage specification that contributes to crypt maintenance, establishing a role for intracellular pH dynamics in cell fate decisions within an adult stem cell lineage.
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Affiliation(s)
- Yi Liu
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Efren Reyes
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA, 94143, USA
| | - David Castillo-Azofeifa
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA, 94143, USA
- Immunology Discovery, Genentech, Inc., South San Francisco, CA, 94080, USA
| | - Ophir D Klein
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Todd Nystul
- Departments of Anatomy, University of California San Francisco, San Francisco, CA, 94143, USA.
| | - Diane L Barber
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, 94143, USA.
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9
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Gong YY, Shao H, Li Y, Brafford P, Stine ZE, Sun J, Felsher DW, Orange JS, Albelda SM, Dang CV. Na +/H +-exchanger 1 enhances antitumor activity of engineered NK-92 natural killer cells. CANCER RESEARCH COMMUNICATIONS 2022; 2:842-856. [PMID: 36380966 PMCID: PMC9648415 DOI: 10.1158/2767-9764.crc-22-0270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 06/16/2023]
Abstract
Adoptive cell transfer (ACT) immunotherapy has remarkable efficacy against some hematological malignancies. However, its efficacy in solid tumors is limited by the adverse tumor microenvironment (TME) conditions, most notably that acidity inhibits T and natural killer (NK) cell mTOR complex 1 (mTORC1) activity and impairs cytotoxicity. In several reported studies, systemic buffering of tumor acidity enhanced the efficacy of immune checkpoint inhibitors. Paradoxically, we found in a c-Myc-driven hepatocellular carcinoma model that systemic buffering increased tumor mTORC1 activity, negating inhibition of tumor growth by anti-PD1 treatment. Therefore, in this proof-of-concept study, we tested the metabolic engineering of immune effector cells to mitigate the inhibitory effect of tumor acidity while avoiding side effects associated with systemic buffering. We first overexpressed an activated RHEB in the human NK cell line NK-92, thereby rescuing acid-blunted mTORC1 activity and enhancing cytolytic activity. Then, to directly mitigate the effect of acidity, we ectopically expressed acid extruder proteins. Whereas ectopic expression of carbonic anhydrase IX (CA9) moderately increased mTORC1 activity, it did not enhance effector function. In contrast, overexpressing a constitutively active Na+/H+-exchanger 1 (NHE1; SLC9A1) in NK-92 did not elevate mTORC1 but enhanced degranulation, target engagement, in vitro cytotoxicity, and in vivo antitumor activity. Our findings suggest the feasibility of overcoming the inhibitory effect of the TME by metabolically engineering immune effector cells, which can enhance ACT for better efficacy against solid tumors.
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Affiliation(s)
- Yao-Yu Gong
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Yu Li
- Department of Pediatrics, Columbia University Medical Center, New York, New York
| | | | | | - Jing Sun
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Dean W. Felsher
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Jordan S. Orange
- Department of Pediatrics, Columbia University Medical Center, New York, New York
| | - Steven M. Albelda
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Chi V. Dang
- The Wistar Institute, Philadelphia, Pennsylvania
- Ludwig Institute for Cancer Research, New York, New York
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10
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Dvorak V, Wiedmer T, Ingles-Prieto A, Altermatt P, Batoulis H, Bärenz F, Bender E, Digles D, Dürrenberger F, Heitman LH, IJzerman AP, Kell DB, Kickinger S, Körzö D, Leippe P, Licher T, Manolova V, Rizzetto R, Sassone F, Scarabottolo L, Schlessinger A, Schneider V, Sijben HJ, Steck AL, Sundström H, Tremolada S, Wilhelm M, Wright Muelas M, Zindel D, Steppan CM, Superti-Furga G. An Overview of Cell-Based Assay Platforms for the Solute Carrier Family of Transporters. Front Pharmacol 2021; 12:722889. [PMID: 34447313 PMCID: PMC8383457 DOI: 10.3389/fphar.2021.722889] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/19/2021] [Indexed: 12/12/2022] Open
Abstract
The solute carrier (SLC) superfamily represents the biggest family of transporters with important roles in health and disease. Despite being attractive and druggable targets, the majority of SLCs remains understudied. One major hurdle in research on SLCs is the lack of tools, such as cell-based assays to investigate their biological role and for drug discovery. Another challenge is the disperse and anecdotal information on assay strategies that are suitable for SLCs. This review provides a comprehensive overview of state-of-the-art cellular assay technologies for SLC research and discusses relevant SLC characteristics enabling the choice of an optimal assay technology. The Innovative Medicines Initiative consortium RESOLUTE intends to accelerate research on SLCs by providing the scientific community with high-quality reagents, assay technologies and data sets, and to ultimately unlock SLCs for drug discovery.
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Affiliation(s)
- Vojtech Dvorak
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alvaro Ingles-Prieto
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Helena Batoulis
- Drug Discovery Sciences–Lead Discovery, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Felix Bärenz
- Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, Germany
| | - Eckhard Bender
- Drug Discovery Sciences–Lead Discovery, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Daniela Digles
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | | | - Laura H. Heitman
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | - Adriaan P. IJzerman
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | - Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Stefanie Kickinger
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Daniel Körzö
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Philipp Leippe
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Thomas Licher
- Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, Germany
| | | | | | | | | | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Vanessa Schneider
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Hubert J. Sijben
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | | | | | | | | | - Marina Wright Muelas
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Diana Zindel
- Drug Discovery Sciences–Lead Discovery, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Claire M. Steppan
- Pfizer Worldwide Research, Development and Medical, Groton, MA, United States
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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11
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Dong Y, Gao Y, Ilie A, Kim D, Boucher A, Li B, Zhang XC, Orlowski J, Zhao Y. Structure and mechanism of the human NHE1-CHP1 complex. Nat Commun 2021; 12:3474. [PMID: 34108458 PMCID: PMC8190280 DOI: 10.1038/s41467-021-23496-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/29/2021] [Indexed: 02/05/2023] Open
Abstract
Sodium/proton exchanger 1 (NHE1) is an electroneutral secondary active transporter present on the plasma membrane of most mammalian cells and plays critical roles in regulating intracellular pH and volume homeostasis. Calcineurin B-homologous protein 1 (CHP1) is an obligate binding partner that promotes NHE1 biosynthetic maturation, cell surface expression and pH-sensitivity. Dysfunctions of either protein are associated with neurological disorders. Here, we elucidate structures of the human NHE1-CHP1 complex in both inward- and inhibitor (cariporide)-bound outward-facing conformations. We find that NHE1 assembles as a symmetrical homodimer, with each subunit undergoing an elevator-like conformational change during cation exchange. The cryo-EM map reveals the binding site for the NHE1 inhibitor cariporide, illustrating how inhibitors block transport activity. The CHP1 molecule differentially associates with these two conformational states of each NHE1 monomer, and this association difference probably underlies the regulation of NHE1 pH-sensitivity by CHP1.
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Affiliation(s)
- Yanli Dong
- grid.9227.e0000000119573309National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yiwei Gao
- grid.9227.e0000000119573309National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Alina Ilie
- grid.14709.3b0000 0004 1936 8649Department of Physiology, McGill University, Montreal, QC Canada
| | - DuSik Kim
- grid.14709.3b0000 0004 1936 8649Department of Physiology, McGill University, Montreal, QC Canada
| | - Annie Boucher
- grid.14709.3b0000 0004 1936 8649Department of Physiology, McGill University, Montreal, QC Canada
| | - Bin Li
- grid.9227.e0000000119573309National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xuejun C. Zhang
- grid.9227.e0000000119573309National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - John Orlowski
- grid.14709.3b0000 0004 1936 8649Department of Physiology, McGill University, Montreal, QC Canada
| | - Yan Zhao
- grid.9227.e0000000119573309National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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12
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An acidic residue buried in the dimer interface of isocitrate dehydrogenase 1 (IDH1) helps regulate catalysis and pH sensitivity. Biochem J 2021; 477:2999-3018. [PMID: 32729927 DOI: 10.1042/bcj20200311] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 12/19/2022]
Abstract
Isocitrate dehydrogenase 1 (IDH1) catalyzes the reversible NADP+-dependent conversion of isocitrate to α-ketoglutarate (αKG) to provide critical cytosolic substrates and drive NADPH-dependent reactions like lipid biosynthesis and glutathione regeneration. In biochemical studies, the forward reaction is studied at neutral pH, while the reverse reaction is typically characterized in more acidic buffers. This led us to question whether IDH1 catalysis is pH-regulated, which would have functional implications under conditions that alter cellular pH, like apoptosis, hypoxia, cancer, and neurodegenerative diseases. Here, we show evidence of catalytic regulation of IDH1 by pH, identifying a trend of increasing kcat values for αKG production upon increasing pH in the buffers we tested. To understand the molecular determinants of IDH1 pH sensitivity, we used the pHinder algorithm to identify buried ionizable residues predicted to have shifted pKa values. Such residues can serve as pH sensors, with changes in protonation states leading to conformational changes that regulate catalysis. We identified an acidic residue buried at the IDH1 dimer interface, D273, with a predicted pKa value upshifted into the physiological range. D273 point mutations had decreased catalytic efficiency and, importantly, loss of pH-regulated catalysis. Based on these findings, we conclude that IDH1 activity is regulated, at least in part, by pH. We show this regulation is mediated by at least one buried acidic residue ∼12 Å from the IDH1 active site. By establishing mechanisms of regulation of this well-conserved enzyme, we highlight catalytic features that may be susceptible to pH changes caused by cell stress and disease.
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13
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Rowe JB, Kapolka NJ, Taghon GJ, Morgan WM, Isom DG. The evolution and mechanism of GPCR proton sensing. J Biol Chem 2021; 296:100167. [PMID: 33478938 PMCID: PMC7948426 DOI: 10.1074/jbc.ra120.016352] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/02/2020] [Accepted: 12/09/2020] [Indexed: 12/13/2022] Open
Abstract
Of the 800 G protein-coupled receptors (GPCRs) in humans, only three (GPR4, GPR65, and GPR68) regulate signaling in acidified microenvironments by sensing protons (H+). How these receptors have uniquely obtained this ability is unknown. Here, we show these receptors evolved the capability to sense H+ signals by acquiring buried acidic residues. Using our informatics platform pHinder, we identified a triad of buried acidic residues shared by all three receptors, a feature distinct from all other human GPCRs. Phylogenetic analysis shows the triad emerged in GPR65, the immediate ancestor of GPR4 and GPR68. To understand the evolutionary and mechanistic importance of these triad residues, we developed deep variant profiling, a yeast-based technology that utilizes high-throughput CRISPR to build and profile large libraries of GPCR variants. Using deep variant profiling and GPCR assays in HEK293 cells, we assessed the pH-sensing contributions of each triad residue in all three receptors. As predicted by our calculations, most triad mutations had profound effects consistent with direct regulation of receptor pH sensing. In addition, we found that an allosteric modulator of many class A GPCRs, Na+, synergistically regulated pH sensing by maintaining the pKa values of triad residues within the physiologically relevant pH range. As such, we show that all three receptors function as coincidence detectors of H+ and Na+. Taken together, these findings elucidate the molecular evolution and long-sought mechanism of GPR4, GPR65, and GPR68 pH sensing and provide pH-insensitive variants that should be valuable for assessing the therapeutic potential and (patho)physiological importance of GPCR pH sensing.
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Affiliation(s)
- Jacob B Rowe
- The Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Nicholas J Kapolka
- The Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Geoffrey J Taghon
- The Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - William M Morgan
- The Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Daniel G Isom
- The Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida, USA; The Department of Tumor Biology, University of Miami Sylvester Comprehensive Cancer Center, Miami, Florida, USA; The Institute for Data Science Computing, University of Miami, Coral Gables, Florida, USA.
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14
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Hendus-Altenburger R, Vogensen J, Pedersen ES, Luchini A, Araya-Secchi R, Bendsoe AH, Prasad NS, Prestel A, Cardenas M, Pedraz-Cuesta E, Arleth L, Pedersen SF, Kragelund BB. The intracellular lipid-binding domain of human Na +/H + exchanger 1 forms a lipid-protein co-structure essential for activity. Commun Biol 2020; 3:731. [PMID: 33273619 PMCID: PMC7713384 DOI: 10.1038/s42003-020-01455-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 11/03/2020] [Indexed: 12/03/2022] Open
Abstract
Dynamic interactions of proteins with lipid membranes are essential regulatory events in biology, but remain rudimentarily understood and particularly overlooked in membrane proteins. The ubiquitously expressed membrane protein Na+/H+-exchanger 1 (NHE1) regulates intracellular pH (pHi) with dysregulation linked to e.g. cancer and cardiovascular diseases. NHE1 has a long, regulatory cytosolic domain carrying a membrane-proximal region described as a lipid-interacting domain (LID), yet, the LID structure and underlying molecular mechanisms are unknown. Here we decompose these, combining structural and biophysical methods, molecular dynamics simulations, cellular biotinylation- and immunofluorescence analysis and exchanger activity assays. We find that the NHE1-LID is intrinsically disordered and, in presence of membrane mimetics, forms a helical αα-hairpin co-structure with the membrane, anchoring the regulatory domain vis-a-vis the transport domain. This co-structure is fundamental for NHE1 activity, as its disintegration reduced steady-state pHi and the rate of pHi recovery after acid loading. We propose that regulatory lipid-protein co-structures may play equally important roles in other membrane proteins.
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Affiliation(s)
- Ruth Hendus-Altenburger
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen Ø, Denmark
| | - Jens Vogensen
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen Ø, Denmark
| | - Emilie Skotte Pedersen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Alessandra Luchini
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Raul Araya-Secchi
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Anne H Bendsoe
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen Ø, Denmark
| | - Nanditha Shyam Prasad
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen Ø, Denmark
| | - Andreas Prestel
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Marité Cardenas
- Biofilms Research Center for Biointerfaces, Malmö University, Per Albin Hanssons Väg 35, 214 32, Malmö, Sweden
| | - Elena Pedraz-Cuesta
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen Ø, Denmark
| | - Lise Arleth
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark.
| | - Stine F Pedersen
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen Ø, Denmark.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark.
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15
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16
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Pedersen SF, Counillon L. The SLC9A-C Mammalian Na +/H + Exchanger Family: Molecules, Mechanisms, and Physiology. Physiol Rev 2019; 99:2015-2113. [PMID: 31507243 DOI: 10.1152/physrev.00028.2018] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Na+/H+ exchangers play pivotal roles in the control of cell and tissue pH by mediating the electroneutral exchange of Na+ and H+ across cellular membranes. They belong to an ancient family of highly evolutionarily conserved proteins, and they play essential physiological roles in all phyla. In this review, we focus on the mammalian Na+/H+ exchangers (NHEs), the solute carrier (SLC) 9 family. This family of electroneutral transporters constitutes three branches: SLC9A, -B, and -C. Within these, each isoform exhibits distinct tissue expression profiles, regulation, and physiological roles. Some of these transporters are highly studied, with hundreds of original articles, and some are still only rudimentarily understood. In this review, we present and discuss the pioneering original work as well as the current state-of-the-art research on mammalian NHEs. We aim to provide the reader with a comprehensive view of core knowledge and recent insights into each family member, from gene organization over protein structure and regulation to physiological and pathophysiological roles. Particular attention is given to the integrated physiology of NHEs in the main organ systems. We provide several novel analyses and useful overviews, and we pinpoint main remaining enigmas, which we hope will inspire novel research on these highly versatile proteins.
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Affiliation(s)
- S F Pedersen
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark; and Université Côte d'Azur, CNRS, Laboratoire de Physiomédecine Moléculaire, LP2M, France, and Laboratories of Excellence Ion Channel Science and Therapeutics, Nice, France
| | - L Counillon
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark; and Université Côte d'Azur, CNRS, Laboratoire de Physiomédecine Moléculaire, LP2M, France, and Laboratories of Excellence Ion Channel Science and Therapeutics, Nice, France
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17
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Spatiotemporal pH Heterogeneity as a Promoter of Cancer Progression and Therapeutic Resistance. Cancers (Basel) 2019; 11:cancers11071026. [PMID: 31330859 PMCID: PMC6678451 DOI: 10.3390/cancers11071026] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 12/15/2022] Open
Abstract
Dysregulation of pH in solid tumors is a hallmark of cancer. In recent years, the role of altered pH heterogeneity in space, between benign and aggressive tissues, between individual cancer cells, and between subcellular compartments, has been steadily elucidated. Changes in temporal pH-related processes on both fast and slow time scales, including altered kinetics of bicarbonate-CO2 exchange and its effects on pH buffering and gradual, progressive changes driven by changes in metabolism, are further implicated in phenotypic changes observed in cancers. These discoveries have been driven by advances in imaging technologies. This review provides an overview of intra- and extracellular pH alterations in time and space reflected in cancer cells, as well as the available technology to study pH spatiotemporal heterogeneity.
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18
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Walton ZE, Brooks RC, Dang CV. mTOR Senses Intracellular pH through Lysosome Dispersion from RHEB. Bioessays 2019; 41:e1800265. [PMID: 31157925 PMCID: PMC6730656 DOI: 10.1002/bies.201800265] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/18/2019] [Indexed: 02/04/2023]
Abstract
Acidity, generated in hypoxia or hypermetabolic states, perturbs homeostasis and is a feature of solid tumors. That acid peripherally disperses lysosomes is a three-decade-old observation, yet one little understood or appreciated. However, recent work has recognized the inhibitory impact this spatial redistribution has on mechanistic target of rapamycin complex 1 (mTORC1), a key regulator of metabolism. This finding argues for a paradigm shift in localization of mTORC1 activator Ras homolog enriched in brain (RHEB), a conclusion several others have now independently reached. Thus, mTORC1, known to sense amino acids, mitogens, and energy to restrict biosynthesis to times of adequate resources, also senses pH and, via dampened mTOR-governed synthesis of clock proteins, regulates the circadian clock to achieve concerted responses to metabolic stress. While this may allow cancer to endure metabolic deprivation, immune cell mTOR signaling likewise exhibits pH sensitivity, suggesting that suppression of antitumor immune function by solid tumor acidity may additionally fuel cancers, an obstacle potentially reversible through therapeutic pH manipulation.
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Affiliation(s)
| | | | - Chi V. Dang
- Ludwig Institute for Cancer Research, New York, NY 10017
- The Wistar Institute, Philadelphia, PA 19104
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19
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Charafeddine RA, Cortopassi WA, Lak P, Tan R, McKenney RJ, Jacobson MP, Barber DL, Wittmann T. Tau repeat regions contain conserved histidine residues that modulate microtubule-binding in response to changes in pH. J Biol Chem 2019; 294:8779-8790. [PMID: 30992364 DOI: 10.1074/jbc.ra118.007004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 04/13/2019] [Indexed: 12/20/2022] Open
Abstract
Tau, a member of the MAP2/tau family of microtubule-associated proteins, stabilizes and organizes axonal microtubules in healthy neurons. In neurodegenerative tauopathies, tau dissociates from microtubules and forms neurotoxic extracellular aggregates. MAP2/tau family proteins are characterized by three to five conserved, intrinsically disordered repeat regions that mediate electrostatic interactions with the microtubule surface. Here, we used molecular dynamics, microtubule-binding experiments, and live-cell microscopy, revealing that highly-conserved histidine residues near the C terminus of each microtubule-binding repeat are pH sensors that can modulate tau-microtubule interaction strength within the physiological intracellular pH range. We observed that at low pH (<7.5), these histidines are positively charged and interact with phenylalanine residues in a hydrophobic cleft between adjacent tubulin dimers. At higher pH (>7.5), tau deprotonation decreased binding to microtubules both in vitro and in cells. Electrostatic and hydrophobic characteristics of histidine were both required for tau-microtubule binding, as substitutions with constitutively and positively charged nonaromatic lysine or uncharged alanine greatly reduced or abolished tau-microtubule binding. Consistent with these findings, tau-microtubule binding was reduced in a cancer cell model with increased intracellular pH but was rapidly restored by decreasing the pH to normal levels. These results add detailed insights into the intracellular regulation of tau activity that may be relevant in both normal and pathological conditions.
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Affiliation(s)
- Rabab A Charafeddine
- From the Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California 94143
| | - Wilian A Cortopassi
- the Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158, and
| | - Parnian Lak
- the Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158, and
| | - Ruensern Tan
- the Department of Molecular and Cellular Biology, University of California Davis, Davis, California 95616
| | - Richard J McKenney
- the Department of Molecular and Cellular Biology, University of California Davis, Davis, California 95616
| | - Matthew P Jacobson
- the Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158, and
| | - Diane L Barber
- From the Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California 94143
| | - Torsten Wittmann
- From the Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California 94143,
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20
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Graham WV, He W, Marchiando AM, Zha J, Singh G, Li HS, Biswas A, Ong MLDM, Jiang ZH, Choi W, Zuccola H, Wang Y, Griffith J, Wu J, Rosenberg HJ, Wang Y, Snapper SB, Ostrov D, Meredith SC, Miller LW, Turner JR. Intracellular MLCK1 diversion reverses barrier loss to restore mucosal homeostasis. Nat Med 2019; 25:690-700. [PMID: 30936544 PMCID: PMC6461392 DOI: 10.1038/s41591-019-0393-7] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 02/08/2019] [Indexed: 01/08/2023]
Abstract
Epithelial barrier loss is a driver of intestinal and systemic diseases. Myosin light chain kinase (MLCK) is a key effector of barrier dysfunction and a potential therapeutic target, but enzymatic inhibition has unacceptable toxicities. Here, we show that a unique domain within the MLCK splice-variant MLCK1 directs perijunctional actomyosin ring (PAMR) recruitment. Using the domain structure and multiple screens, we identified a domain-binding small molecule (Divertin) that blocks MLCK1 recruitment without inhibiting enzymatic function. Divertin blocks acute, TNF-induced MLCK1 recruitment as well as downstream MLC phosphorylation, barrier loss, and diarrhea in vitro and in vivo. Divertin corrects barrier dysfunction and prevents disease development and progression in experimental inflammatory bowel disease. Beyond applications of Divertin in gastrointestinal disease, this general approach to enzymatic inhibition by preventing access to specific subcellular sites provides a new paradigm for safely and precisely targeting individual properties of enzymes with multiple functions.
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Affiliation(s)
- W Vallen Graham
- Department of Pathology, University of Chicago, Chicago, IL, USA.,Laboratory of Chemical Biology & Signal Transduction, The Rockefeller University, New York, NY, USA
| | - Weiqi He
- Department of Pathology, University of Chicago, Chicago, IL, USA.,Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Suda Genomic Resource Center, Soochow University, and Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | | | - Juanmin Zha
- Department of Pathology, University of Chicago, Chicago, IL, USA.,Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Suda Genomic Resource Center, Soochow University, and Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Gurminder Singh
- Department of Pathology, University of Chicago, Chicago, IL, USA.,Laboratory of Mucosal Barrier Pathobiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hua-Shan Li
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Suda Genomic Resource Center, Soochow University, and Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Amlan Biswas
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ma Lora Drizella M Ong
- Laboratory of Mucosal Barrier Pathobiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Zhi-Hui Jiang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Suda Genomic Resource Center, Soochow University, and Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Wangsun Choi
- Laboratory of Mucosal Barrier Pathobiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Yitang Wang
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | | | - Jingshing Wu
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | | | - Yingmin Wang
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Scott B Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - David Ostrov
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, College of Medicine, Gainesville, FL, USA
| | | | - Lawrence W Miller
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Jerrold R Turner
- Department of Pathology, University of Chicago, Chicago, IL, USA. .,Laboratory of Mucosal Barrier Pathobiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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21
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Jensen HH, Pedersen GA, Morgen JJ, Parsons M, Pedersen SF, Nejsum LN. The Na + /H + exchanger NHE1 localizes as clusters to cryptic lamellipodia and accelerates collective epithelial cell migration. J Physiol 2018; 597:849-867. [PMID: 30471113 DOI: 10.1113/jp277383] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 11/16/2018] [Indexed: 12/12/2022] Open
Abstract
KEY POINTS Exogenous Na+ /H+ exchanger 1 (NHE1) expression stimulated the collective migration of epithelial cell sheets Stimulation with epidermal growth factor, a key morphogen, primarily increased migration of the front row of cells, whereas NHE1 increased that of submarginal cell rows, and the two stimuli were additive Accordingly, NHE1 localized not only to the leading edges of leader cells, but also in cryptic lamellipodia in submarginal cell rows NHE1 expression disrupted the morphology of epithelial cell sheets and three-dimensional cysts ABSTRACT: Collective cell migration plays essential roles in embryonic development, in normal epithelial repair processes, and in many diseases including cancer. The Na+ /H+ exchanger 1 (NHE1, SLC9A1) is an important regulator of motility in many cells and has been widely studied for its roles in cancer, although its possible role in collective migration of normal epithelial cells has remained unresolved. In the present study, we show that NHE1 expression in MDCK-II kidney epithelial cells accelerated collective cell migration. NHE1 localized to the leading edges of leader cells, as well as to cryptic lamellipodia in submarginal cell rows. Epidermal growth factor, a kidney morphogen, increased displacement of the front row of collectively migrating cells and reduced the number of migration fingers. NHE1 expression increased the number of migration fingers and increased displacement of submarginal cell rows, resulting in additive effects of NHE1 and epidermal growth factor. Finally, NHE1 expression resulted in disorganized development of MDCK-II cell cysts. Thus, NHE1 contributes to collective migration and epithelial morphogenesis, suggesting roles for the transporter in embryonic and early postnatal development.
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Affiliation(s)
- Helene H Jensen
- Department of Clinical Medicine, Aarhus University, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, Denmark.,Department of Chemistry and Bioscience, Aalborg University, Denmark
| | | | - Jeanette J Morgen
- Department of Clinical Medicine, Aarhus University, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Maddy Parsons
- Randall Division of Cell and Molecular Biophysics, King's College London, UK
| | - Stine F Pedersen
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Denmark
| | - Lene N Nejsum
- Department of Clinical Medicine, Aarhus University, Denmark
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22
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White KA, Grillo-Hill BK, Esquivel M, Peralta J, Bui VN, Chire I, Barber DL. β-Catenin is a pH sensor with decreased stability at higher intracellular pH. J Cell Biol 2018; 217:3965-3976. [PMID: 30315137 PMCID: PMC6219716 DOI: 10.1083/jcb.201712041] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 07/16/2018] [Accepted: 08/31/2018] [Indexed: 02/08/2023] Open
Abstract
White et al. find that intracellular pH regulates the stability of β-catenin, the Wnt signaling molecule that controls cell polarity, adhesion, and differentiation. A conserved histidine residue in β-catenin mediates pH-dependent binding to the E3 ligase β-TrCP for degradation, and a cancer-associated mutation that bypasses this pH-sensitive regulation induces ectopic tumors in the Drosophila eye. β-Catenin functions as an adherens junction protein for cell–cell adhesion and as a signaling protein. β-catenin function is dependent on its stability, which is regulated by protein–protein interactions that stabilize β-catenin or target it for proteasome-mediated degradation. In this study, we show that β-catenin stability is regulated by intracellular pH (pHi) dynamics, with decreased stability at higher pHi in both mammalian cells and Drosophila melanogaster. β-Catenin degradation requires phosphorylation of N-terminal residues for recognition by the E3 ligase β-TrCP. While β-catenin phosphorylation was pH independent, higher pHi induced increased β-TrCP binding and decreased β-catenin stability. An evolutionarily conserved histidine in β-catenin (found in the β-TrCP DSGIHS destruction motif) is required for pH-dependent binding to β-TrCP. Expressing a cancer-associated H36R–β-catenin mutant in the Drosophila eye was sufficient to induce Wnt signaling and produced pronounced tumors not seen with other oncogenic β-catenin alleles. We identify pHi dynamics as a previously unrecognized regulator of β-catenin stability, functioning in coincidence with phosphorylation.
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Affiliation(s)
- Katharine A White
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA
| | - Bree K Grillo-Hill
- Department of Biological Sciences, San Jose State University, San Jose, CA
| | - Mario Esquivel
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA
| | - Jobelle Peralta
- Department of Biological Sciences, San Jose State University, San Jose, CA
| | - Vivian N Bui
- Department of Biological Sciences, San Jose State University, San Jose, CA
| | - Ismahan Chire
- Department of Biological Sciences, San Jose State University, San Jose, CA
| | - Diane L Barber
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA
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23
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White KA, Ruiz DG, Szpiech ZA, Strauli NB, Hernandez RD, Jacobson MP, Barber DL. Cancer-associated arginine-to-histidine mutations confer a gain in pH sensing to mutant proteins. Sci Signal 2017; 10:10/495/eaam9931. [PMID: 28874603 DOI: 10.1126/scisignal.aam9931] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The intracellular pH (pHi) of most cancers is constitutively higher than that of normal cells and enhances proliferation and cell survival. We found that increased pHi enabled the tumorigenic behaviors caused by somatic arginine-to-histidine mutations, which are frequent in cancer and confer pH sensing not seen with wild-type proteins. Experimentally raising the pHi increased the activity of R776H mutant epidermal growth factor receptor (EGFR-R776H), thereby increasing proliferation and causing transformation in fibroblasts. An Arg-to-Gly mutation did not confer these effects. Molecular dynamics simulations of EGFR suggested that decreased protonation of His776 at high pH causes conformational changes in the αC helix that may stabilize the active form of the kinase. An Arg-to-His, but not Arg-to-Lys, mutation in the transcription factor p53 (p53-R273H) decreased its transcriptional activity and attenuated the DNA damage response in fibroblasts and breast cancer cells with high pHi. Lowering pHi attenuated the tumorigenic effects of both EGFR-R776H and p53-R273H. Our data suggest that some somatic mutations may confer a fitness advantage to the higher pHi of cancer cells.
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Affiliation(s)
- Katharine A White
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Diego Garrido Ruiz
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Zachary A Szpiech
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nicolas B Strauli
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA.,Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Diane L Barber
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA.
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Szpiech ZA, Strauli NB, White KA, Ruiz DG, Jacobson MP, Barber DL, Hernandez RD. Prominent features of the amino acid mutation landscape in cancer. PLoS One 2017; 12:e0183273. [PMID: 28837668 PMCID: PMC5570307 DOI: 10.1371/journal.pone.0183273] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/01/2017] [Indexed: 01/20/2023] Open
Abstract
Cancer can be viewed as a set of different diseases with distinctions based on tissue origin, driver mutations, and genetic signatures. Accordingly, each of these distinctions have been used to classify cancer subtypes and to reveal common features. Here, we present a different analysis of cancer based on amino acid mutation signatures. Non-negative Matrix Factorization and principal component analysis of 29 cancers revealed six amino acid mutation signatures, including four signatures that were dominated by either arginine to histidine (Arg>His) or glutamate to lysine (Glu>Lys) mutations. Sample-level analyses reveal that while some cancers are heterogeneous, others are largely dominated by one type of mutation. Using a non-overlapping set of samples from the COSMIC somatic mutation database, we validate five of six mutation signatures, including signatures with prominent arginine to histidine (Arg>His) or glutamate to lysine (Glu>Lys) mutations. This suggests that our classification of cancers based on amino acid mutation patterns may provide avenues of inquiry pertaining to specific protein mutations that may generate novel insights into cancer biology.
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Affiliation(s)
- Zachary A. Szpiech
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States of America
- * E-mail: (RDH); (ZAS)
| | - Nicolas B. Strauli
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States of America
- Biomedical Sciences Graduate Program, University of California, San Francisco, United States of America
| | - Katharine A. White
- Department of Cell and Tissue Biology, University of California, San Francisco, United States of America
| | - Diego Garrido Ruiz
- Department of Pharmaceutical Chemistry, University of California, San Francisco, United States of America
| | - Matthew P. Jacobson
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States of America
- Department of Pharmaceutical Chemistry, University of California, San Francisco, United States of America
| | - Diane L. Barber
- Department of Cell and Tissue Biology, University of California, San Francisco, United States of America
| | - Ryan D. Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, United States of America
- Quantitative Biosciences Institute, University of California, San Francisco, United States of America
- Institute for Human Genetics, University of California, San Francisco, United States of America
- * E-mail: (RDH); (ZAS)
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