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Liefting EJM, Bajramovic JJ. Optimizing Wnt activation in fetal calf serum (FCS)-free organoid expansion media. FRONTIERS IN TOXICOLOGY 2025; 7:1504469. [PMID: 40438536 PMCID: PMC12116640 DOI: 10.3389/ftox.2025.1504469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Accepted: 04/30/2025] [Indexed: 06/01/2025] Open
Abstract
Organoid technology can revolutionize biomedical research by increasing the translational value of experimental results while at the same time reducing the need for experimental animal use. However, in most cases the organoid culture workflow relies on expansion media that contain fetal calf serum (FCS). The production of FCS causes animal suffering, and the use of it is hampered by factors that negatively impact the reproducibility (such as the large inter-batch variation and the undefined composition of FCS), relevance (such as the induction of a non-physiological cellular phenotype), as well as the clinical translatability (such as the potential to cause xeno-immunization or to contain xenogeneic pathogens). There is thus a strong impetus to find animal-free alternatives to the use of FCS. Most contemporary expansion media for organoid culture are not FCS-free. This is mainly contributable to the use of FCS for the recombinant production of the growth factor Wnt3A. Wnt3A-conditioned medium is added to expansion media to induce Wnt signaling, which is necessary for organoid proliferation. In turn, FCS is pivotal to stabilize and solubilize the Wnt3A protein, and not perse for the survival, adhesion or proliferation of cells. This mini-review explores alternative methods to induce Wnt signaling in organoid expansion media, encompassing the use of soluble Wnt mimetics, the use of carriers, and the use of small molecule inhibitors. Ultimately, alternative Wnt activation approaches for different experimental goals are reviewed and discussed.
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Kollerits B, Kotsis F, Schneider MP, Schultheiss UT, Weissensteiner H, Schönherr S, Forer L, Meiselbach H, Wanner C, Eckardt KU, Dieplinger H, Kronenberg F. Association of Serum Afamin Concentrations With Kidney Failure in Patients With CKD: Findings From the German CKD Cohort Study. Am J Kidney Dis 2025; 85:432-441.e1. [PMID: 39743167 DOI: 10.1053/j.ajkd.2024.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 10/29/2024] [Accepted: 11/14/2024] [Indexed: 01/04/2025]
Abstract
RATIONALE & OBJECTIVE Afamin is a vitamin E-binding glycoprotein primarily expressed in the liver and kidney. This study investigated whether serum afamin concentrations are associated with kidney function and incident kidney failure. STUDY DESIGN Prospective cohort study with 6.5 years follow-up. SETTING & PARTICIPANTS 5,041 White patients enrolled in the German Chronic Kidney Disease (GCKD) study with measured afamin concentrations and either an estimated glomerular filtration rate (eGFR) of 30-60mL/min/1.73m2 or an eGFR>60mL/min/1.73m2 with a urinary albumin-creatinine ratio (UACR) of≥300mg/g at study entry. EXPOSURE Serum afamin concentrations (mg/L). OUTCOME Incident kidney failure (initiation of kidney replacement therapy or kidney-related death). ANALYTICAL APPROACH Generalized linear regression and quantile regression models fit to investigate the association of afamin concentrations with eGFR and UACR. Adjusted Cox regression analysis to examine the association of afamin concentrations with incident kidney failure. RESULTS The mean±SD afamin concentration at study entry was 73.2±17.6mg/L. Higher afamin concentrations were associated with better kidney function with a 2.60mL/min/1.73m2 higher eGFR (95% CI, 2.30-2.89) and a 5.97mg/g lower UACR (95% CI, 3.04-8.90) for each 10mg/L higher level of afamin concentration in adjusted analysis. During the follow-up period, each 10mg/L higher level of afamin concentration was associated with a 14% lower risk of kidney failure (HR, 0.86 [95%CI, 0.81-0.92], P<0.001). LIMITATIONS Residual confounding, and potential limited generalizability to non-White populations and people with mild stages of chronic kidney disease (CKD) or no CKD. CONCLUSIONS Higher serum afamin concentrations appear to be associated with a higher eGFR, less albuminuria, and a lower risk for future kidney failure in patients with CKD.
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Affiliation(s)
- Barbara Kollerits
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Fruzsina Kotsis
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg; Department of Medicine IV, Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg
| | - Markus P Schneider
- Department of Nephrology and Hypertension, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen
| | - Ulla T Schultheiss
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg; Department of Medicine IV, Nephrology and Primary Care, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg
| | - Hansi Weissensteiner
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Lukas Forer
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Heike Meiselbach
- Department of Nephrology and Hypertension, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen
| | - Christoph Wanner
- Division of Nephrology, Department of Internal Medicine I, University Hospital Würzburg, Würzburg
| | - Kai-Uwe Eckardt
- Department of Nephrology and Hypertension, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen; Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Hans Dieplinger
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria.
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3
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Chideriotis S, Anastasiadi AT, Tzounakas VL, Fortis SP, Kriebardis AG, Valsami S. Morphogens and Cell-Derived Structures (Exosomes and Cytonemes) as Components of the Communication Between Cells. Int J Mol Sci 2025; 26:881. [PMID: 39940651 PMCID: PMC11816454 DOI: 10.3390/ijms26030881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2024] [Revised: 01/16/2025] [Accepted: 01/18/2025] [Indexed: 02/16/2025] Open
Abstract
Morphogens, which are non-classical transcription factors, according to several studies, display a crucial role in tissue patterning, organ architecture establishment, and human disease pathogenesis. Recent advances have expanded the morphogen participation to a wide range of human diseases. There are many genetic syndromes caused by mutations of components of morphogen signaling pathways. The aberrant morphogen pathways also promote cancer cell maintenance, renewal, proliferation, and migration. On the other hand, exosomes and their application in the biomedical field are of evolving significance. The evidence that membrane structures participate in the creation of morphogenic gradience and biodistribution of morphogen components renders them attractive as new therapeutic tools. This intercellular morphogen transport is performed by cell-derived structures, mainly exosomes and cytonemes, and extracellular substances like heparan sulphate proteoglycans and lipoproteins. The interaction between morphogens and Extracellular Vesicles has been observed at first in the most studied insect, Drosophila, and afterwards analogous findings have been proved in vertebrates. This review presents the protagonists and mechanisms of lipid-modified morphogens (Hedgehog and Wnt/β-catenin) biodistribution.
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Affiliation(s)
| | - Alkmini T. Anastasiadi
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (A.T.A.); (V.L.T.)
| | - Vassilis L. Tzounakas
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (A.T.A.); (V.L.T.)
| | - Sotirios P. Fortis
- Laboratory of Reliability and Quality Control in Laboratory Hematology (HemQcR), Department of Biomedical Sciences, School of Health & Caring Sciences, University of West Attica (UniWA), 12243 Egaleo, Greece; (S.P.F.); (A.G.K.)
| | - Anastasios G. Kriebardis
- Laboratory of Reliability and Quality Control in Laboratory Hematology (HemQcR), Department of Biomedical Sciences, School of Health & Caring Sciences, University of West Attica (UniWA), 12243 Egaleo, Greece; (S.P.F.); (A.G.K.)
| | - Serena Valsami
- Hematology Laboratory, Blood Bank, Aretaieion Hospital, National and Kapodistrian University of Athens, 11528 Athens, Greece
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4
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Holzem M, Boutros M, Holstein TW. The origin and evolution of Wnt signalling. Nat Rev Genet 2024; 25:500-512. [PMID: 38374446 DOI: 10.1038/s41576-024-00699-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2024] [Indexed: 02/21/2024]
Abstract
The Wnt signal transduction pathway has essential roles in the formation of the primary body axis during development, cellular differentiation and tissue homeostasis. This animal-specific pathway has been studied extensively in contexts ranging from developmental biology to medicine for more than 40 years. Despite its physiological importance, an understanding of the evolutionary origin and primary function of Wnt signalling has begun to emerge only recently. Recent studies on very basal metazoan species have shown high levels of conservation of components of both canonical and non-canonical Wnt signalling pathways. Furthermore, some pathway proteins have been described also in non-animal species, suggesting that recruitment and functional adaptation of these factors has occurred in metazoans. In this Review, we summarize the current state of research regarding the evolutionary origin of Wnt signalling, its ancestral function and the characteristics of the primal Wnt ligand, with emphasis on the importance of genomic studies in various pre-metazoan and basal metazoan species.
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Affiliation(s)
- Michaela Holzem
- Division of Signalling and Functional Genomics, German Cancer Research Centre (DKFZ), Heidelberg, Germany.
- Department of Cell and Molecular Biology & BioQuant, Heidelberg University, Heidelberg, Germany.
- Faculty of Medicine Mannheim, Heidelberg University, Heidelberg, Germany.
- Institute for Human Genetics, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany.
| | - Michael Boutros
- Division of Signalling and Functional Genomics, German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Department of Cell and Molecular Biology & BioQuant, Heidelberg University, Heidelberg, Germany
- Faculty of Medicine Mannheim, Heidelberg University, Heidelberg, Germany
- Institute for Human Genetics, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Thomas W Holstein
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany.
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Van Pee T, Martens DS, Alfano R, Engelen L, Sleurs H, Rasking L, Plusquin M, Nawrot TS. Cord Blood Proteomic Profiles, Birth Weight, and Early Life Growth Trajectories. JAMA Netw Open 2024; 7:e2411246. [PMID: 38743419 PMCID: PMC11094560 DOI: 10.1001/jamanetworkopen.2024.11246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/13/2024] [Indexed: 05/16/2024] Open
Abstract
Importance The cord blood proteome, a repository of proteins derived from both mother and fetus, might offer valuable insights into the physiological and pathological state of the fetus. However, its association with birth weight and growth trajectories early in life remains unexplored. Objective To identify cord blood proteins associated with birth weight and the birth weight ratio (BWR) and to evaluate the associations of these cord blood proteins with early growth trajectories. Design, Setting, and Participants This cohort study included 288 mother-child pairs from the ongoing prospective Environmental Influence on Early Aging birth cohort study. Newborns were recruited from East-Limburg Hospital in Genk, Belgium, between February 2010 and November 2017 and followed up until ages 4 to 6 years. Data were analyzed from February 2022 to September 2023. Main Outcomes and Measures The outcome of interest was the associations of 368 inflammatory-related cord blood proteins with birth weight or BWR and with early life growth trajectories (ie, rapid growth at age 12 months and weight, body mass index [BMI] z score, waist circumference, and overweight at age 4-6 years) using multiple linear regression models. The BWR was calculated by dividing the birth weight by the median birth weight of the population-specific reference growth curve, considering parity, sex, and gestational age. Results are presented as estimates or odds ratios (ORs) for each doubling in proteins. Results The sample included 288 infants (125 [43.4%] male; mean [SD] gestation age, 277.2 [11.6] days). The mean (SD) age of the child at the follow-up examination was 4.6 (0.4) years old. After multiple testing correction, there were significant associations of birth weight and BWR with 7 proteins: 2 positive associations: afamin (birth weight: coefficient, 341.16 [95% CI, 192.76 to 489.50]) and secreted frizzled-related protein 4 (SFRP4; birth weight: coefficient, 242.60 [95% CI, 142.77 to 342.43]; BWR: coefficient, 0.07 [95% CI, 0.04 to 0.10]) and 5 negative associations: cadherin EGF LAG 7-pass G-type receptor 2 (CELSR2; birth weight: coefficient, -237.52 [95% CI, -343.15 to -131.89]), ephrin type-A receptor 4 (EPHA4; birth weight: coefficient, -342.78 [95% CI, -463.10 to -222.47]; BWR: coefficient, -0.11 [95% CI, -0.14 to -0.07]), SLIT and NTRK-like protein 1 (SLITRK1; birth weight: coefficient, -366.32 [95% CI, -476.66 to -255.97]; BWR: coefficient, -0.11 [95% CI, -0.15 to -0.08]), transcobalamin-1 (TCN1; birth weight: coefficient, -208.75 [95% CI, -305.23 to -112.26]), and unc-5 netrin receptor D (UNC5D; birth weight: coefficient, -209.27 [95% CI, -295.14 to -123.40]; BWR: coefficient, -0.07 [95% CI, -0.09 to -0.04]). Further evaluation showed that 2 proteins were still associated with rapid growth at age 12 months (afamin: OR, 0.32 [95% CI, 0.11-0.88]; TCN1: OR, 2.44 [95% CI, 1.26-4.80]). At age 4 to 6 years, CELSR2, EPHA4, SLITRK1, and UNC5D were negatively associated with weight (coefficients, -1.33 to -0.68 kg) and body mass index z score (coefficients, -0.41 to -0.23), and EPHA4, SLITRK1, and UNC5D were negatively associated with waist circumference (coefficients, -1.98 to -0.87 cm). At ages 4 to 6 years, afamin (OR, 0.19 [95% CI, 0.05-0.70]) and SLITRK1 (OR, 0.32 [95% CI, 0.10-0.99]) were associated with lower odds for overweight. Conclusions and Relevance This cohort study found 7 cord blood proteins associated with birth weight and growth trajectories early in life. Overall, these findings suggest that stressors that could affect the cord blood proteome during pregnancy might have long-lasting associations with weight and body anthropometrics.
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Affiliation(s)
- Thessa Van Pee
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Dries S. Martens
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Rossella Alfano
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Liesa Engelen
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Hanne Sleurs
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Leen Rasking
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Tim S. Nawrot
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
- Department of Public Health and Primary Care, Leuven University, Leuven, Belgium
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6
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Arredondo SB, Valenzuela-Bezanilla D, Santibanez SH, Varela-Nallar L. Wnt signaling in the adult hippocampal neurogenic niche. Stem Cells 2022; 40:630-640. [PMID: 35446432 DOI: 10.1093/stmcls/sxac027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/29/2022] [Indexed: 11/14/2022]
Abstract
The subgranular zone (SGZ) of the hippocampal dentate gyrus (DG) is a neurogenic niche of the adult brain that contains neural stem cells (NSCs) able to generate excitatory glutamatergic granule neurons, which integrate into the DG circuit and contribute to hippocampal plasticity, learning, and memory. Thus, endogenous NSCs could be harnessed for therapeutic purposes. In this context, it is critical to characterize the molecular mechanisms controlling the generation and functional integration of adult-born neurons. Adult hippocampal neurogenesis is tightly controlled by both cell-autonomous mechanisms and the interaction with the complex niche microenvironment, which harbors the NSCs and provides the signals to support their maintenance, activation, and differentiation. Among niche-derived factors, Wnt ligands play diverse roles. Wnts are secreted glycoproteins that bind to Frizzled receptors and co-receptors to trigger the Wnt signaling pathway. Here, we summarize the current knowledge about the roles of Wnts in the regulation of adult hippocampal neurogenesis. We discuss the possible contribution of the different niche cells to the regulation of local Wnt signaling activity, and how Wnts derived from different cell types could induce differential effects. Finally, we discuss how the effects of Wnt signaling on hippocampal network activity might contribute to neurogenesis regulation. Although the evidence supports relevant roles for Wnt signaling in adult hippocampal neurogenesis, defining the cellular source and the mechanisms controlling secretion and diffusion of Wnts will be crucial to further understand Wnt signaling regulation of adult NSCs, and eventually, to propose this pathway as a therapeutic target to promote neurogenesis.
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Affiliation(s)
- Sebastian B Arredondo
- Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Echaurren 183, 8370071, Santiago, Chile
| | - Daniela Valenzuela-Bezanilla
- Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Echaurren 183, 8370071, Santiago, Chile
| | - Sebastian H Santibanez
- Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Echaurren 183, 8370071, Santiago, Chile
| | - Lorena Varela-Nallar
- Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Echaurren 183, 8370071, Santiago, Chile
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7
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Broussard EM, Rodriguez ZB, Austin CC. Evolution of the albumin protein family in reptiles. Mol Phylogenet Evol 2022; 169:107435. [DOI: 10.1016/j.ympev.2022.107435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 10/19/2022]
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8
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An itch for things remote: The journey of Wnts. Curr Top Dev Biol 2022; 150:91-128. [DOI: 10.1016/bs.ctdb.2022.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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9
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Gross JC. Extracellular WNTs: Trafficking, Exosomes, and Ligand-Receptor Interaction. Handb Exp Pharmacol 2021; 269:29-43. [PMID: 34505202 DOI: 10.1007/164_2021_531] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
WNT signaling is a key developmental pathway in tissue organization. A recent focus of research is the secretion of WNT proteins from source cells. Research over the past decade on how WNTs are produced and released into the extracellular space has unravelled very specific control mechanisms in the early secretory pathway, specialized trafficking routes, and redundant forms of packaging for delivery to target cells. In this review I discuss the findings that WNT proteins have been found on extracellular vesicles (EVs) such as exosomes and possible functional implications. There is an ongoing debate in the WNT signaling field whether EV are relevant in vivo and can fulfill specific functions, also fueled by the general preconception of EV secretion as cellular garbage disposal. As part of the EV research community, I want to give an overview of what we know and don't know about WNT secretion on EVs and offer a more unifying model that can explain current discrepancies in observations regarding WNT secretion.
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Affiliation(s)
- Julia Christina Gross
- Developmental Biochemistry, University Medical Center Goettingen, Goettingen, Germany. .,Hematology and Oncology, University Medical Center Goettingen, Goettingen, Germany. .,Health and Medical University Potsdam, Potsdam, Germany.
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10
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Markham L, Tolbert JD, Kull FJ, Midgett CR, Micalizio GC. An Enantiodefined Conformationally Constrained Fatty Acid Mimetic and Potent Inhibitor of ToxT. ACS Med Chem Lett 2021; 12:1493-1497. [PMID: 34531958 PMCID: PMC8436414 DOI: 10.1021/acsmedchemlett.1c00378] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/20/2021] [Indexed: 11/29/2022] Open
Abstract
The chiral conformation that palmitoleic acid takes when it is bound to ToxT, the master regulator of virulence genes in the bacterial pathogen Vibrio cholerae, was used as inspiration to design a novel class of fatty acid mimetics. The best mimetic, based on a chiral hydrindane, was found to be a potent inhibitor of this target. The synthetic chemistry that enabled these studies was based on the sequential use of a stereoselective annulative cross-coupling reaction and dissolving metal reduction to establish the C13 and C9 stereocenters, respectively.
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Affiliation(s)
- Lauren
E. Markham
- Department of Chemistry, Dartmouth College, Burke Laboratory, Hanover, New Hampshire 03755, United States
| | - Jessica D. Tolbert
- Department of Chemistry, Dartmouth College, Burke Laboratory, Hanover, New Hampshire 03755, United States
| | - F. Jon Kull
- Department of Chemistry, Dartmouth College, Burke Laboratory, Hanover, New Hampshire 03755, United States
| | - Charles R. Midgett
- Department of Chemistry, Dartmouth College, Burke Laboratory, Hanover, New Hampshire 03755, United States
| | - Glenn C. Micalizio
- Department of Chemistry, Dartmouth College, Burke Laboratory, Hanover, New Hampshire 03755, United States
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11
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Organoids and Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13112657. [PMID: 34071313 PMCID: PMC8197877 DOI: 10.3390/cancers13112657] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/20/2021] [Accepted: 05/24/2021] [Indexed: 12/12/2022] Open
Abstract
Organoids were first established as a three-dimensional cell culture system from mouse small intestine. Subsequent development has made organoids a key system to study many human physiological and pathological processes that affect a variety of tissues and organs. In particular, organoids are becoming very useful tools to dissect colorectal cancer (CRC) by allowing the circumvention of classical problems and limitations, such as the impossibility of long-term culture of normal intestinal epithelial cells and the lack of good animal models for CRC. In this review, we describe the features and current knowledge of intestinal organoids and how they are largely contributing to our better understanding of intestinal cell biology and CRC genetics. Moreover, recent data show that organoids are appropriate systems for antitumoral drug testing and for the personalized treatment of CRC patients.
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12
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Dhasmana D, Veerapathiran S, Azbazdar Y, Nelanuthala AVS, Teh C, Ozhan G, Wohland T. Wnt3 Is Lipidated at Conserved Cysteine and Serine Residues in Zebrafish Neural Tissue. Front Cell Dev Biol 2021; 9:671218. [PMID: 34124053 PMCID: PMC8189181 DOI: 10.3389/fcell.2021.671218] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/28/2021] [Indexed: 12/22/2022] Open
Abstract
Wnt proteins are a family of hydrophobic cysteine-rich secreted glycoproteins that regulate a gamut of physiological processes involved in embryonic development and tissue homeostasis. Wnt ligands are post-translationally lipidated in the endoplasmic reticulum (ER), a step essential for its membrane targeting, association with lipid domains, secretion and interaction with receptors. However, at which residue(s) Wnts are lipidated remains an open question. Initially it was proposed that Wnts are lipid-modified at their conserved cysteine and serine residues (C77 and S209 in mWnt3a), and mutations in either residue impedes its secretion and activity. Conversely, some studies suggested that serine is the only lipidated residue in Wnts, and substitution of serine with alanine leads to retention of Wnts in the ER. In this work, we investigate whether in zebrafish neural tissues Wnt3 is lipidated at one or both conserved residues. To this end, we substitute the homologous cysteine and serine residues of zebrafish Wnt3 with alanine (C80A and S212A) and investigate their influence on Wnt3 membrane organization, secretion, interaction and signaling activity. Collectively, our results indicate that Wnt3 is lipid modified at its C80 and S212 residues. Further, we find that lipid addition at either C80 or S212 is sufficient for its secretion and membrane organization, while the lipid modification at S212 is indispensable for receptor interaction and signaling.
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Affiliation(s)
- Divya Dhasmana
- Department of Biological Sciences and Center for BioImaging Sciences, National University of Singapore, Singapore, Singapore
| | - Sapthaswaran Veerapathiran
- Department of Biological Sciences and Center for BioImaging Sciences, National University of Singapore, Singapore, Singapore
| | - Yagmur Azbazdar
- Izmir Biomedicine and Genome Center (IBG), Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute (IBG-Izmir), Dokuz Eylul University, Izmir, Turkey
| | | | - Cathleen Teh
- Department of Biological Sciences and Center for BioImaging Sciences, National University of Singapore, Singapore, Singapore
| | - Gunes Ozhan
- Izmir Biomedicine and Genome Center (IBG), Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute (IBG-Izmir), Dokuz Eylul University, Izmir, Turkey
| | - Thorsten Wohland
- Department of Biological Sciences and Center for BioImaging Sciences, National University of Singapore, Singapore, Singapore
- Department of Chemistry, National University of Singapore, Singapore, Singapore
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13
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Waibl F, Liedl KR, Rupp B. Correcting cis-trans-transgressions in macromolecular structure models. FEBS J 2021; 289:2793-2804. [PMID: 33880875 DOI: 10.1111/febs.15884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/01/2021] [Accepted: 04/16/2021] [Indexed: 11/27/2022]
Abstract
Many macromolecular X-ray and cryo-EM structure models deposited in the PDB contain biologically relevant small molecule ligands with unsaturated fatty acid acyl chains, whose cis-trans stereochemistry is incorrect. The molecules are either not properly defined in their stereochemical restraint files, or the proper stereochemistry is neglected during model building. Often, the same molecules appear in deposited models in both isomeric configurations, one of which is almost always incorrect, and the use of the same moiety (HET) identifier and restraint files in model refinement is wrong. We present case studies of frequently occurring molecules and a compilation of identified cases of C-C=C-C cis-trans geometry in the deposited structure models. Full listings of cis/trans torsion angles are provided for models with commonly occurring molecules to assist identification and correction of cis-trans errors and prevent inadvertent use of incorrect models. Caveats for users, advice for modellers and suggestions for remediation efforts with a simple but effective restraint file modification are provided.
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Affiliation(s)
- Franz Waibl
- Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Klaus R Liedl
- Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Bernhard Rupp
- k. -k.Hofkristallamt, San Diego, CA, USA.,Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
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14
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Ge H, Zhang B, Li T, Yu Y, Men F, Zhao S, Liu J, Zhang T. Potential targets and the action mechanism of food-derived dipeptides on colitis: network pharmacology and bioinformatics analysis. Food Funct 2021; 12:5989-6000. [DOI: 10.1039/d1fo00469g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The present study provides an efficient method for screening food-derived dipeptides to attenuate colitis based on the network pharmacology and bioinformatics analysis.
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Affiliation(s)
- Huifang Ge
- Jilin Provincial Key Laboratory of Nutrition and Functional Food
- Jilin University
- Changchun
- People's Republic of China
- College of Food Science and Engineering
| | - Biying Zhang
- Jilin Provincial Key Laboratory of Nutrition and Functional Food
- Jilin University
- Changchun
- People's Republic of China
- College of Food Science and Engineering
| | - Ting Li
- Jilin Provincial Key Laboratory of Nutrition and Functional Food
- Jilin University
- Changchun
- People's Republic of China
- College of Food Science and Engineering
| | - Yue Yu
- Jilin Provincial Key Laboratory of Nutrition and Functional Food
- Jilin University
- Changchun
- People's Republic of China
- College of Food Science and Engineering
| | - Fangbing Men
- Jilin Provincial Key Laboratory of Nutrition and Functional Food
- Jilin University
- Changchun
- People's Republic of China
- College of Food Science and Engineering
| | - Songning Zhao
- Jilin Provincial Key Laboratory of Nutrition and Functional Food
- Jilin University
- Changchun
- People's Republic of China
- College of Food Science and Engineering
| | - Jingbo Liu
- Jilin Provincial Key Laboratory of Nutrition and Functional Food
- Jilin University
- Changchun
- People's Republic of China
- College of Food Science and Engineering
| | - Ting Zhang
- Jilin Provincial Key Laboratory of Nutrition and Functional Food
- Jilin University
- Changchun
- People's Republic of China
- College of Food Science and Engineering
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15
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Veerapathiran S, Teh C, Zhu S, Kartigayen I, Korzh V, Matsudaira PT, Wohland T. Wnt3 distribution in the zebrafish brain is determined by expression, diffusion and multiple molecular interactions. eLife 2020; 9:e59489. [PMID: 33236989 PMCID: PMC7725503 DOI: 10.7554/elife.59489] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 11/23/2020] [Indexed: 12/19/2022] Open
Abstract
Wnt3 proteins are lipidated and glycosylated signaling molecules that play an important role in zebrafish neural patterning and brain development. However, the transport mechanism of lipid-modified Wnts through the hydrophilic extracellular environment for long-range action remains unresolved. Here we determine how Wnt3 accomplishes long-range distribution in the zebrafish brain. First, we characterize the Wnt3-producing source and Wnt3-receiving target regions. Subsequently, we analyze Wnt3 mobility at different length scales by fluorescence correlation spectroscopy and fluorescence recovery after photobleaching. We demonstrate that Wnt3 spreads extracellularly and interacts with heparan sulfate proteoglycans (HSPG). We then determine the binding affinity of Wnt3 to its receptor, Frizzled1 (Fzd1), using fluorescence cross-correlation spectroscopy and show that the co-receptor, low-density lipoprotein receptor-related protein 5 (Lrp5), is required for Wnt3-Fzd1 interaction. Our results are consistent with the extracellular distribution of Wnt3 by a diffusive mechanism that is modified by tissue morphology, interactions with HSPG, and Lrp5-mediated receptor binding, to regulate zebrafish brain development.
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Affiliation(s)
- Sapthaswaran Veerapathiran
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
- Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Cathleen Teh
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
- Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Shiwen Zhu
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
- Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Indira Kartigayen
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
- Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Vladimir Korzh
- International Institute of Molecular and Cell Biology in WarsawWarsawPoland
| | - Paul T Matsudaira
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
- Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Thorsten Wohland
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
- Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
- Department of Chemistry, National University of SingaporeSingaporeSingapore
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16
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Wallace J, Narasipura SD, Sha BE, French AL, Al-Harthi L. Canonical Wnts Mediate CD8 + T Cell Noncytolytic Anti-HIV-1 Activity and Correlate with HIV-1 Clinical Status. THE JOURNAL OF IMMUNOLOGY 2020; 205:2046-2055. [PMID: 32887752 DOI: 10.4049/jimmunol.1801379] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 08/04/2020] [Indexed: 11/19/2022]
Abstract
CD8+ T cells do not rely solely on cytotoxic functions for significant HIV control. Moreover, the noncytotoxic CD8+ T cell antiviral response is a primary mediator of natural HIV control such as that seen in HIV elite controllers and long-term nonprogressors that does not require combined antiretroviral therapy. In this study, we investigated the biological factors contributing to the noncytotoxic control of HIV replication mediated by primary human CD8+ T cells. We report that canonical Wnt signaling inhibits HIV transcription in an MHC-independent, noncytotoxic manner and that mediators of this pathway correlate with HIV controller clinical status. We show that CD8+ T cells express all 19 Wnts and CD8+ T cell-conditioned medium (CM) induced canonical Wnt signaling in infected recipient cells while simultaneously inhibiting HIV transcription. Antagonizing canonical Wnt activity in CD8+ T cell CM resulted in increased HIV transcription in infected cells. Further, Wnt2b expression was upregulated in HIV controllers versus viremic patients, and in vitro depletion of Wnt2b and/or Wnt9b from CD8+ CM reversed HIV inhibitory activity. Finally, plasma concentration of Dkk-1, an antagonist of canonical Wnt signaling, was higher in viremic patients with lower CD4 counts. This study demonstrates that canonical Wnt signaling inhibits HIV and significantly correlates with HIV controller status.
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Affiliation(s)
- Jennillee Wallace
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL 60612
| | - Srinivas D Narasipura
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL 60612
| | - Beverly E Sha
- Division of Infectious Diseases, Rush University Medical Center, Chicago, IL 60612
| | - Audrey L French
- Division of Infectious Diseases, Rush University Medical Center, Chicago, IL 60612.,Stroger Hospital of Cook County, Cook County Health and Hospitals System, Chicago, IL 60612; and.,Ruth M. Rothstein CORE Center, Cook County Health and Hospitals System, Chicago, IL 60612
| | - Lena Al-Harthi
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL 60612;
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17
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Zulkiflee NS, Awang SA, Ming WX, Kamilan MFW, Mariappan MY, Kit TJ. In Silico Docking of Vitamin E Isomers on Transport Proteins. Curr Comput Aided Drug Des 2020; 16:467-472. [DOI: 10.2174/1573409915666190614113733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/30/2019] [Accepted: 05/07/2019] [Indexed: 11/22/2022]
Abstract
Background:
Vitamin E is comprised of α, β, γ and δ-tocopherols (Ts) and α, β, γ and δ-
tocotrienols (T3s). Vitamin E has neuroprotective antioxidant, anti-cancer, and cholesterol-lowering
effects. Intracellular trafficking of these isomers remains largely unknown, except for αT which is
selectively transported by αT transfer protein (αTTP).
Objective:
This study aimed to determine the binding of vitamin E isomers on transport proteins
using in silico docking.
Methods:
Transport proteins were selected using AmiGo Gene Ontology tool based on the same
molecular function annotation as αTTP. Protein structures were obtained from the Protein Data
Bank. Ligands structures were obtained from ZINC database. In silico docking was performed
using SwissDock.
Results and Discussion:
A total of 6 transport proteins were found: SEC14-like protein 2,
glycolipid transfer protein (GLTP), pleckstrin homology domain-containing family A member 8,
collagen type IV alpha-3-binding protein, ceramide-1-phosphate transfer protein and afamin.
Compared with other transport proteins, αTTP had the highest affinities for all isomers except βT3.
Binding order of vitamin E isomers toward αTTP was γT > βT > αT > δT > αT3 > γT3 > δT3 > βT3.
GLTP had a higher affinity for tocotrienols than tocopherols. βT3 bound stronger to GLTP than αTTP.
Conclusion:
αTTP remained as the most preferred transport protein for most of the isomers. The
binding affinity of αT toward αTTP was not the highest than other isomers suggested that other
intracellular trafficking mechanisms of these isomers may exist. GLTP may mediate the intracellular
transport of tocotrienols, especially βT3. Improving the bioavailability of these isomers may enhance
their beneficial effects to human.
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Affiliation(s)
- Nurul Syeefa Zulkiflee
- Department of Biochemistry, Faculty of Medicine, Universiti Kebangsaan Malaysia, 56000 Cheras, Malaysia
| | - Siti Amilia Awang
- Department of Biochemistry, Faculty of Medicine, Universiti Kebangsaan Malaysia, 56000 Cheras, Malaysia
| | - Woo Xian Ming
- Department of Biochemistry, Faculty of Medicine, Universiti Kebangsaan Malaysia, 56000 Cheras, Malaysia
| | | | - M Yuveneshwari Mariappan
- Department of Biochemistry, Faculty of Medicine, Universiti Kebangsaan Malaysia, 56000 Cheras, Malaysia
| | - Tan Jen Kit
- Department of Biochemistry, Faculty of Medicine, Universiti Kebangsaan Malaysia, 56000 Cheras, Malaysia
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18
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Rushton E, Kopke DL, Broadie K. Extracellular heparan sulfate proteoglycans and glycan-binding lectins orchestrate trans-synaptic signaling. J Cell Sci 2020; 133:133/15/jcs244186. [PMID: 32788209 DOI: 10.1242/jcs.244186] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The exceedingly narrow synaptic cleft (<20 nm) and adjacent perisynaptic extracellular space contain an astonishing array of secreted and membrane-anchored glycoproteins. A number of these extracellular molecules regulate intercellular trans-synaptic signaling by binding to ligands, acting as co-receptors or modulating ligand-receptor interactions. Recent work has greatly expanded our understanding of extracellular proteoglycan and glycan-binding lectin families as key regulators of intercellular signaling at the synapse. These secreted proteins act to regulate the compartmentalization of glycoprotein ligands and receptors, crosslink dynamic extracellular and cell surface lattices, modulate both exocytosis and endocytosis vesicle cycling, and control postsynaptic receptor trafficking. Here, we focus closely on the Drosophila glutamatergic neuromuscular junction (NMJ) as a model synapse for understanding extracellular roles of the many heparan sulfate proteoglycan (HSPG) and lectin proteins that help determine synaptic architecture and neurotransmission strength. We particularly concentrate on the roles of extracellular HSPGs and lectins in controlling trans-synaptic signaling, especially that mediated by the Wnt and BMP pathways. These signaling mechanisms are causally linked to a wide spectrum of neurological disease states that impair coordinated movement and cognitive functions.
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Affiliation(s)
- Emma Rushton
- Department of Biological Sciences, Brain Institute, and Kennedy Center for Research on Human Development, Vanderbilt University, Nashville, TN 37235, USA
| | - Danielle L Kopke
- Department of Biological Sciences, Brain Institute, and Kennedy Center for Research on Human Development, Vanderbilt University, Nashville, TN 37235, USA
| | - Kendal Broadie
- Department of Biological Sciences, Brain Institute, and Kennedy Center for Research on Human Development, Vanderbilt University, Nashville, TN 37235, USA
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19
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Naschberger A, Juyoux P, von Velsen J, Rupp B, Bowler MW. Controlled dehydration, structural flexibility and gadolinium MRI contrast compound binding in the human plasma glycoprotein afamin. Acta Crystallogr D Struct Biol 2019; 75:1071-1083. [PMID: 31793901 PMCID: PMC6889915 DOI: 10.1107/s2059798319013500] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/02/2019] [Indexed: 01/29/2023] Open
Abstract
Afamin, which is a human blood plasma glycoprotein, a putative multifunctional transporter of hydrophobic molecules and a marker for metabolic syndrome, poses multiple challenges for crystallographic structure determination, both practically and in analysis of the models. Several hundred crystals were analysed, and an unusual variability in cell volume and difficulty in solving the structure despite an ∼34% sequence identity with nonglycosylated human serum albumin indicated that the molecule exhibits variable and context-sensitive packing, despite the simplified glycosylation in insect cell-expressed recombinant afamin. Controlled dehydration of the crystals was able to stabilize the orthorhombic crystal form, reducing the number of molecules in the asymmetric unit from the monoclinic form and changing the conformational state of the protein. An iterative strategy using fully automatic experiments available on MASSIF-1 was used to quickly determine the optimal protocol to achieve the phase transition, which should be readily applicable to many types of sample. The study also highlights the drawback of using a single crystallographic structure model for computational modelling purposes given that the conformational state of the binding sites and the electron density in the binding site, which is likely to result from PEGs, greatly varies between models. This also holds for the analysis of nonspecific low-affinity ligands, where often a variety of fragments with similar uncertainty can be modelled, inviting interpretative bias. As a promiscuous transporter, afamin also seems to bind gadoteridol, a magnetic resonance imaging contrast compound, in at least two sites. One pair of gadoteridol molecules is located near the human albumin Sudlow site, and a second gadoteridol molecule is located at an intermolecular site in proximity to domain IA. The data from the co-crystals support modern metrics of data quality in the context of the information that can be gleaned from data sets that would be abandoned on classical measures.
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Affiliation(s)
- Andreas Naschberger
- Department of Genetic Epidemiology, Medical University Innsbruck, Schöpfstrasse 41, A-6020 Innsbruck, Austria
| | - Pauline Juyoux
- Grenoble Outstation, European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Jill von Velsen
- Grenoble Outstation, European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Bernhard Rupp
- Department of Genetic Epidemiology, Medical University Innsbruck, Schöpfstrasse 41, A-6020 Innsbruck, Austria
- C.V.M.O., k. k. Hofkristallamt, 991 Audrey Place, Vista, California, USA
| | - Matthew W. Bowler
- Grenoble Outstation, European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
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20
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Svensson O, Gilski M, Nurizzo D, Bowler MW. A comparative anatomy of protein crystals: lessons from the automatic processing of 56 000 samples. IUCRJ 2019; 6:822-831. [PMID: 31576216 PMCID: PMC6760449 DOI: 10.1107/s2052252519008017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 06/04/2019] [Indexed: 05/12/2023]
Abstract
The fully automatic processing of crystals of macromolecules has presented a unique opportunity to gather information on the samples that is not usually recorded. This has proved invaluable in improving sample-location, characterization and data-collection algorithms. After operating for four years, MASSIF-1 has now processed over 56 000 samples, gathering information at each stage, from the volume of the crystal to the unit-cell dimensions, the space group, the quality of the data collected and the reasoning behind the decisions made in data collection. This provides an unprecedented opportunity to analyse these data together, providing a detailed landscape of macromolecular crystals, intimate details of their contents and, importantly, how the two are related. The data show that mosaic spread is unrelated to the size or shape of crystals and demonstrate experimentally that diffraction intensities scale in proportion to crystal volume and molecular weight. It is also shown that crystal volume scales inversely with molecular weight. The results set the scene for the development of X-ray crystallography in a changing environment for structural biology.
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Affiliation(s)
- Olof Svensson
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, F-38043 Grenoble, France
| | - Maciej Gilski
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, F-38042 Grenoble, France
| | - Didier Nurizzo
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, F-38043 Grenoble, France
| | - Matthew W. Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, F-38042 Grenoble, France
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21
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Abstract
Wnt proteins are secreted glycoproteins that regulate multiple processes crucial to the development and tissue homeostasis of multicellular organisms, including tissue patterning, proliferation, cell fate specification, cell polarity and migration. To elicit these effects, Wnts act as autocrine as well as paracrine signalling molecules between Wnt-producing and Wnt-receiving cells. More than 40 years after the discovery of the Wg/Wnt pathway, it is still unclear how they are transported to fulfil their paracrine signalling functions. Several mechanisms have been proposed to mediate intercellular Wnt transport, including Wnt-binding proteins, lipoproteins, exosomes and cytonemes. In this Review, we describe the evidence for each proposed mechanism, and discuss how they may contribute to Wnt dispersal in tissue-specific and context-dependent manners, to regulate embryonic development precisely and maintain the internal steady state within a defined tissue.
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Affiliation(s)
- Daniel Routledge
- Living Systems Institute, Biosciences, College of Life and Environmental Science, University of Exeter, Exeter EX4 4QD, UK
| | - Steffen Scholpp
- Living Systems Institute, Biosciences, College of Life and Environmental Science, University of Exeter, Exeter EX4 4QD, UK
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22
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Abstract
Wnt signaling proteins are fatty-acylated and bind to the protein afamin. The afamin-Wnt complex increases Wnt solubility dramatically and is likely involved in Wnt trafficking. In this issue of Structure, Naschberger et al. (2017) determine the crystal structure of afamin in complex with palmitoleic acid, revealing how afamin binds palmitoleoylated Wnt.
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Affiliation(s)
- Mark A Wilson
- Department of Biochemistry and Redox Biology Center, University of Nebraska, N118 Beadle Center, Lincoln, NE 68588, USA.
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23
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Abstract
Wnt signaling regulates physiological processes ranging from cell differentiation to bone formation. Dysregulation of Wnt signaling is linked to several human ailments, including colorectal, pancreatic, and breast cancers. As such, modulation of this pathway has been an attractive strategy for therapeutic development of anticancer agents. Since the discovery of Wnt proteins more than 35 years ago, research efforts continue to focus on understanding the biochemistry of their molecular interactions and their biological functions. Wnt is a secreted glycoprotein covalently modified with a cis-unsaturated fatty acyl group at a conserved serine residue, and this modification is required for Wnt secretion and activity. To initiate signaling, Wnt proteins bind to cell-surface Frizzled (FZD) receptors, but the molecular basis for recognition of Wnt's fatty acyl moiety by the extracellular cysteine-rich domain of FZD has become clear only very recently. Here, we review the most recent developments in the field, focusing on structural and biochemical studies of the FZD receptor family and highlighting new insights into their molecular arrangement and mode of regulation by cis-unsaturated fatty acids. Additionally, we examine how other lipid-binding proteins recognize fatty acyl chains on Wnt proteins in the regulation of Wnt secretion and activities. Altogether, this perspective expands our understanding of fatty acid–protein interactions in the FZD system and provides a basis for guiding future research in the field.
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Affiliation(s)
- Aaron H Nile
- From the Department of Early Discovery Biochemistry, Genentech, South San Francisco, California 94080
| | - Rami N Hannoush
- From the Department of Early Discovery Biochemistry, Genentech, South San Francisco, California 94080
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24
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Hosseini V, Dani C, Geranmayeh MH, Mohammadzadeh F, Nazari Soltan Ahmad S, Darabi M. Wnt lipidation: Roles in trafficking, modulation, and function. J Cell Physiol 2018; 234:8040-8054. [PMID: 30341908 DOI: 10.1002/jcp.27570] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 09/17/2018] [Indexed: 12/30/2022]
Abstract
The Wnt signaling pathway consists of various downstream target proteins that have substantial roles in mammalian cell proliferation, differentiation, and development. Its aberrant activity can lead to uncontrolled proliferation and tumorigenesis. The posttranslational connection of fatty acyl chains to Wnt proteins provides the unique capacity for regulation of Wnt activity. In spite of the past belief that Wnt molecules are subject to dual acylation, it has been shown that these proteins have only one acylation site and undergo monounsaturated fatty acylation. The Wnt monounsaturated fatty acyl chain is more than just a hydrophobic coating and appears to be critical for Wnt signaling, transport, and receptor activation. Here, we provide an overview of recent findings in Wnt monounsaturated fatty acylation and the mechanism by which this lipid moiety regulates Wnt activity from the site of production to its receptor interactions.
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Affiliation(s)
- Vahid Hosseini
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Mohammad Hossein Geranmayeh
- Neurosciences Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fatemeh Mohammadzadeh
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Masoud Darabi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Université Côte d'Azur, CNRS, Inserm, iBV, Nice, France
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25
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Svensson O, Gilski M, Nurizzo D, Bowler MW. Multi-position data collection and dynamic beam sizing: recent improvements to the automatic data-collection algorithms on MASSIF-1. Acta Crystallogr D Struct Biol 2018; 74:433-440. [PMID: 29717714 PMCID: PMC5930350 DOI: 10.1107/s2059798318003728] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 03/03/2018] [Indexed: 12/11/2022] Open
Abstract
Macromolecular crystallography is now a mature and widely used technique that is essential in the understanding of biology and medicine. Increases in computing power combined with robotics have not only enabled large numbers of samples to be screened and characterized but have also enabled better decisions to be taken on data collection itself. This led to the development of MASSIF-1 at the ESRF, the first beamline in the world to run fully automatically while making intelligent decisions taking user requirements into account. Since opening in late 2014, the beamline has processed over 42 000 samples. Improvements have been made to the speed of the sample-handling robotics and error management within the software routines. The workflows initially put into place, while highly innovative at the time, have been expanded to include increased complexity and additional intelligence using the information gathered during characterization; this includes adapting the beam diameter dynamically to match the diffraction volume within the crystal. Complex multi-position and multi-crystal data collections have now also been integrated into the selection of experiments available. This has led to increased data quality and throughput, allowing even the most challenging samples to be treated automatically.
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Affiliation(s)
- Olof Svensson
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Maciej Gilski
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
| | - Didier Nurizzo
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, CS 40220, 38043 Grenoble, France
| | - Matthew W. Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble, France
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26
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Altamirano A, Naschberger A, Fürnrohr BG, Saldova R, Struwe WB, Jennings PM, Millán Martín S, Malic S, Plangger I, Lechner S, Pisano R, Peretti N, Linke B, Aguiar MM, Fresser F, Ritsch A, Lenac Rovis T, Goode C, Rudd PM, Scheffzek K, Rupp B, Dieplinger H. Expression, Purification, and Biochemical Characterization of Human Afamin. J Proteome Res 2018; 17:1269-1277. [PMID: 29441788 DOI: 10.1021/acs.jproteome.7b00867] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Afamin is an 87 kDa glycoprotein with five predicted N-glycosylation sites. Afamin's glycan abundance contributes to conformational and chemical inhomogeneity presenting great challenges for molecular structure determination. For the purpose of studying the structure of afamin, various forms of recombinantly expressed human afamin (rhAFM) with different glycosylation patterns were thus created. Wild-type rhAFM and various hypoglycosylated forms were expressed in CHO, CHO-Lec1, and HEK293T cells. Fully nonglycosylated rhAFM was obtained by transfection of point-mutated cDNA to delete all N-glycosylation sites of afamin. Wild-type and hypo/nonglycosylated rhAFM were purified from cell culture supernatants by immobilized metal ion affinity and size exclusion chromatography. Glycan analysis of purified proteins demonstrated differences in micro- and macro-heterogeneity of glycosylation enabling the comparison between hypoglycosylated, wild-type rhAFM, and native plasma afamin. Because antibody fragments can work as artificial chaperones by stabilizing the structure of proteins and consequently enhance the chance for successful crystallization, we incubated a Fab fragment of the monoclonal anti-afamin antibody N14 with human afamin and obtained a stoichiometric complex. Subsequent results showed sufficient expression of various partially or nonglycosylated forms of rhAFM in HEK293T and CHO cells and revealed that glycosylation is not necessary for expression and secretion.
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Affiliation(s)
| | | | | | - Radka Saldova
- NIBRT GlycoScience Group, National Institute for Bioprocessing Research & Training , Dublin, Ireland
| | - Weston B Struwe
- NIBRT GlycoScience Group, National Institute for Bioprocessing Research & Training , Dublin, Ireland
| | - Patrick M Jennings
- NIBRT GlycoScience Group, National Institute for Bioprocessing Research & Training , Dublin, Ireland
| | - Silvia Millán Martín
- NIBRT GlycoScience Group, National Institute for Bioprocessing Research & Training , Dublin, Ireland
| | - Suzana Malic
- Center for Proteomics, Faculty of Medicine, University of Rijeka , 51000 Rijeka, Croatia
| | | | | | | | | | | | | | | | | | - Tihana Lenac Rovis
- Center for Proteomics, Faculty of Medicine, University of Rijeka , 51000 Rijeka, Croatia
| | | | - Pauline M Rudd
- NIBRT GlycoScience Group, National Institute for Bioprocessing Research & Training , Dublin, Ireland
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