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Marrer-Berger E, Nicastri A, Augustin A, Kramar V, Liao H, Hanisch LJ, Carpy A, Weinzierl T, Durr E, Schaub N, Nudischer R, Ortiz-Franyuti D, Breous-Nystrom E, Stucki J, Hobi N, Raggi G, Cabon L, Lezan E, Umaña P, Woodhouse I, Bujotzek A, Klein C, Ternette N. The physiological interactome of TCR-like antibody therapeutics in human tissues. Nat Commun 2024; 15:3271. [PMID: 38627373 PMCID: PMC11021511 DOI: 10.1038/s41467-024-47062-5] [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: 07/05/2022] [Accepted: 03/19/2024] [Indexed: 04/19/2024] Open
Abstract
Selective binding of TCR-like antibodies that target a single tumour-specific peptide antigen presented by human leukocyte antigens (HLA) is the absolute prerequisite for their therapeutic suitability and patient safety. To date, selectivity assessment has been limited to peptide library screening and predictive modeling. We developed an experimental platform to de novo identify interactomes of TCR-like antibodies directly in human tissues using mass spectrometry. As proof of concept, we confirm the target epitope of a MAGE-A4-specific TCR-like antibody. We further determine cross-reactive peptide sequences for ESK1, a TCR-like antibody with known off-target activity, in human liver tissue. We confirm off-target-induced T cell activation and ESK1-mediated liver spheroid killing. Off-target sequences feature an amino acid motif that allows a structural groove-coordination mimicking that of the target peptide, therefore allowing the interaction with the engager molecule. We conclude that our strategy offers an accurate, scalable route for evaluating the non-clinical safety profile of TCR-like antibody therapeutics prior to first-in-human clinical application.
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Affiliation(s)
- Estelle Marrer-Berger
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Annalisa Nicastri
- The Jenner Institute, Old Road Campus Research Building, Oxford, OX37DQ, UK
- Centre for Immuno-Oncology, Old Road Campus Research Building, Oxford, OX37DQ, UK
| | - Angelique Augustin
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Vesna Kramar
- Roche Innovation Center Zürich, 8952, Schlieren, Switzerland
| | - Hanqing Liao
- The Jenner Institute, Old Road Campus Research Building, Oxford, OX37DQ, UK
- Centre for Immuno-Oncology, Old Road Campus Research Building, Oxford, OX37DQ, UK
| | | | - Alejandro Carpy
- Roche Pharma Research & Early Development, Roche Innovation Center Munich, 82377, Penzberg, Germany
| | - Tina Weinzierl
- Roche Innovation Center Zürich, 8952, Schlieren, Switzerland
| | - Evelyne Durr
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Nathalie Schaub
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Ramona Nudischer
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Daniela Ortiz-Franyuti
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Ekaterina Breous-Nystrom
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Janick Stucki
- Alveolix AG, Swiss Organs-on-Chip Innovation, 3010, Bern, Switzerland
| | - Nina Hobi
- Alveolix AG, Swiss Organs-on-Chip Innovation, 3010, Bern, Switzerland
| | - Giulia Raggi
- Alveolix AG, Swiss Organs-on-Chip Innovation, 3010, Bern, Switzerland
| | - Lauriane Cabon
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Emmanuelle Lezan
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Pablo Umaña
- Roche Innovation Center Zürich, 8952, Schlieren, Switzerland
| | - Isaac Woodhouse
- The Jenner Institute, Old Road Campus Research Building, Oxford, OX37DQ, UK
- Centre for Immuno-Oncology, Old Road Campus Research Building, Oxford, OX37DQ, UK
| | - Alexander Bujotzek
- Roche Pharma Research & Early Development, Roche Innovation Center Munich, 82377, Penzberg, Germany
| | - Christian Klein
- Roche Innovation Center Zürich, 8952, Schlieren, Switzerland.
| | - Nicola Ternette
- The Jenner Institute, Old Road Campus Research Building, Oxford, OX37DQ, UK.
- Centre for Immuno-Oncology, Old Road Campus Research Building, Oxford, OX37DQ, UK.
- Department of Pharmaceutical Sciences, University of Utrecht, 3584, CH, Utrecht, The Netherlands.
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Cbl-b deficiency provides protection against UVB-induced skin damage by modulating inflammatory gene signature. Cell Death Dis 2018; 9:835. [PMID: 30082827 PMCID: PMC6079082 DOI: 10.1038/s41419-018-0858-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 06/28/2018] [Accepted: 07/04/2018] [Indexed: 12/17/2022]
Abstract
Exposure of skin to ultraviolet (UV) radiation induces DNA damage, inflammation, and immune suppression that ultimately lead to skin cancer. However, some of the pathways that regulate these events are poorly understood. We exposed mice to UVB to study its early effects in the absence of Cbl-b, a known suppressor of antitumor immune response in the skin. Cbl-b-/- mice were protected from UV-induced cell damage as shown by the lower number of cyclobutane pyrimidine dimers and sunburn cells in exposed skin compared to wild-type mice. Microarray data revealed that deficiency of Cbl-b resulted in differential expression of genes involved in apoptosis evasion, tumor suppression and cell survival in UV-exposed skin. After UVB, Cbl-b-/- mice upregulated gene expression pattern associated with regulation of epidermal cell proliferation linked to Wnt signaling mediators and enzymes that relate to cell removal and tissue remodeling like MMP12. Additionally, the skin of Cbl-b-/- mice was protected from chronic inflammatory responses and epidermal hyperplasia in a 4-weeks UVB treatment protocol. Overall, our results suggest a novel role for Cbl-b in regulating inflammation and physiologic clearance of damaged cells in response to UVB by modulating inflammatory gene signature.
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Wong N, Morahan G, Stathopoulos M, Proietto J, Andrikopoulos S. A novel mechanism regulating insulin secretion involving Herpud1 in mice. Diabetologia 2013; 56:1569-76. [PMID: 23620059 DOI: 10.1007/s00125-013-2908-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 03/18/2013] [Indexed: 11/24/2022]
Abstract
AIMS/HYPOTHESIS Type 2 diabetes results from beta cell dysfunction after prolonged physiological stress, which causes oversecretion of insulin. We recently found that insulin hypersecretion is mediated by at least two genes. Among mouse models of type 2 diabetes, the DBA/2 mouse strain is more susceptible to diabetes than is the C57BL/6J (B6J) strain. One distinctive feature of the DBA/2 mouse is that it hypersecretes insulin, independent of changes in insulin sensitivity; we identified Nnt as a gene responsible for this trait. METHODS To identify the other gene(s) affecting insulin hypersecretion, we tested a panel of recombinant inbred BXD strains, which have different combinations of B6 and DBA/2 alleles. RESULTS We found that 25% of the BXD strains hypersecreted insulin in response to glucose. Microarray profiling of islets from high- and low-secretor strains showed that at least four genes were differentially expressed. One gene was consistently underexpressed in islets from both DBA/2 and the high-secretor BXD strains. This gene (Herpud1 or Herp) encodes the 54 kDa endoplasmic reticulum stress-inducible protein (HERP) that resides in the integral endoplasmic reticulum membrane. To test directly whether Herpud1 can interact with Nnt, Herpud1 was either knocked down or overexpressed in MIN6 cells. These results showed that when Herpud1 was suppressed, Nnt expression was reduced, while overexpression of Herpud1 led to increased Nnt expression. Furthermore, Herpud1 suppression resulted in significantly decreased glucose-stimulated insulin secretion in the DBA/2 islets but not B6J islets. CONCLUSIONS/INTERPRETATION We conclude that Herpud1 regulates insulin secretion via control of Nnt expression.
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Affiliation(s)
- N Wong
- Department of Medicine (Austin Health), Austin Hospital, University of Melbourne, Heidelberg Heights, Melbourne, Victoria, 3084, Australia.
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Sun Z, Cao X, Jiang MM, Qiu Y, Zhou H, Chen L, Qin B, Wu H, Jiang F, Chen J, Liu J, Dai Y, Chen HF, Hu QY, Wu Z, Zeng JZ, Yao XS, Zhang XK. Inhibition of β-catenin signaling by nongenomic action of orphan nuclear receptor Nur77. Oncogene 2011; 31:2653-67. [PMID: 21986938 PMCID: PMC3257393 DOI: 10.1038/onc.2011.448] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Dysregulation of β-catenin turnover due to mutations of its regulatory proteins including adenomatous polyposis coli (APC) and p53 is implicated in the pathogenesis of cancer. Thus, intensive effort is being made to search for alternative approaches to reduce abnormally activated β-catenin in cancer cells. Nur77, an orphan member of the nuclear receptor superfamily, has a role in the growth and apoptosis of cancer cells. Here, we reported that Nur77 could inhibit transcriptional activity of β-catenin by inducing β-catenin degradation via proteasomal degradation pathway that is glycogen synthase kinase 3β and Siah-1 independent. Nur77 induction of β-catenin degradation required both the N-terminal region of Nur77, which was involved in Nur77 ubiquitination, and the C-terminal region, which was responsible for β-catenin binding. Nur77/ΔDBD, a Nur77 mutant lacking its DNA-binding domain, resided in the cytoplasm, interacted with β-catenin, and induced β-catenin degradation, demonstrating that Nur77-mediated β-catenin degradation was independent of its DNA binding and transactivation, and might occur in the cytoplasm. In addition, we reported our identification of two digitalis-like compounds (DLCs), H-9 and ATE-i2-b4, which potently induced Nur77 expression and β-catenin degradation in SW620 colon cancer cells expressing mutant APC protein in vitro and in animals. DLC-induced Nur77 protein was mainly found in the cytoplasm, and inhibition of Nur77 nuclear export by the CRM1-dependent nuclear export inhibitor leptomycin B or Jun N-terminal kinase inhibitor prevented the effect of DLC on inducing β-catenin degradation. Together, our results demonstrate that β-catenin can be degraded by cytoplasmic Nur77 through their interaction and identify H-9 and ATE-i2-b4 as potent activators of the Nur77-mediated pathway for β-catenin degradation.
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Affiliation(s)
- Z Sun
- School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
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Camacho CP, Latini FRM, Oler G, Hojaij FC, Maciel RMB, Riggins GJ, Cerutti JM. Down-regulation of NR4A1 in follicular thyroid carcinomas is restored following lithium treatment. Clin Endocrinol (Oxf) 2009; 70:475-83. [PMID: 18727708 PMCID: PMC2742303 DOI: 10.1111/j.1365-2265.2008.03349.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
INTRODUCTION The identification of follicular thyroid adenoma-associated transcripts will lead to a better understanding of the events involved in pathogenesis and progression of follicular tumours. Using Serial Analysis of Gene Expression, we identified five genes that are absent in a malignant follicular thyroid carcinoma (FTC) library, but expressed in follicular adenoma (FTA) and normal thyroid libraries. METHODS NR4A1, one of the five genes, was validated in a set of 27 normal thyroid tissues, 10 FTAs and 14 FTCs and three thyroid carcinoma cell lines by real time PCR. NR4A1 can be transiently increased by a variety of stimuli, including lithium, which is used as adjuvant therapy of thyroid carcinoma with (131)I. We tested if lithium could restore NR4A1 expression. The expression of other genes potentially involved in the same signalling pathway was tested. To this end, lithium was used at different concentration (10 mm or 20 mm) and time (2 h and 24 h) and the level of expression was tested by quantitative PCR. We next tested if Lithium could affect cell growth and apoptosis. RESULTS We observed that NR4A1 expression was under-expressed in most of the FTCs investigated, compared with expression in normal thyroid tissues and FTAs. We also found a positive correlation between NR4A1 and FOSB gene expression. Lithium induced NR4A1 and FOSB expression, reduced CCDN1 expression, inhibited cell growth and triggered apoptosis in a FTC cell line. CONCLUSIONS NR4A1 is under-expressed in most of FTCs. The loss of expression of both NR4A1 and the Wnt pathway gene FOSB was correlated with malignancy. This is consistent with the hypothesis that its loss of expression is part of the transformation process of FTCs, either as a direct or indirect consequence of Wnt pathway alterations. Lithium restores NR4A1 expression, induces apoptosis and reduces cell growth. These findings may explain a possible molecular mechanism of lithium's therapeutic action.
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MESH Headings
- Adenocarcinoma, Follicular/drug therapy
- Adenocarcinoma, Follicular/metabolism
- Adenocarcinoma, Follicular/pathology
- Adenoma/drug therapy
- Adenoma/metabolism
- Adenoma/pathology
- Apoptosis/drug effects
- Cell Line, Tumor
- Cell Proliferation/drug effects
- Chemotherapy, Adjuvant
- Cyclin D1/genetics
- Cyclin D1/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Dose-Response Relationship, Drug
- Down-Regulation/drug effects
- Humans
- Lithium Compounds/pharmacology
- Lithium Compounds/therapeutic use
- Nuclear Receptor Subfamily 4, Group A, Member 1
- Proto-Oncogene Proteins c-fos/genetics
- Proto-Oncogene Proteins c-fos/metabolism
- Receptors, Steroid/genetics
- Receptors, Steroid/metabolism
- Signal Transduction/drug effects
- Thyroid Neoplasms/drug therapy
- Thyroid Neoplasms/metabolism
- Thyroid Neoplasms/pathology
- Wnt Proteins/genetics
- Wnt Proteins/metabolism
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Affiliation(s)
- Cléber P Camacho
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology, Federal University of São Paulo, São Paulo, Brazil
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Ziegler S, Röhrs S, Tickenbrock L, Langerak A, Chu ST, Feldmann I, Jakubowski N, Müller O. Lipocalin 24p3 is regulated by the Wnt pathway independent of regulation by iron. ACTA ACUST UNITED AC 2007; 174:16-23. [PMID: 17350462 DOI: 10.1016/j.cancergencyto.2006.11.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Revised: 10/27/2006] [Accepted: 11/03/2006] [Indexed: 11/25/2022]
Abstract
Lipocalin 24p3 plays a direct role in iron transport and regulates the levels of important proteins of the iron metabolism. Iron-loaded 24p3 binds to its specific receptor (24p3R) on the cell surface. Upon binding to its receptor, 24p3 is internalized into the cell, where it releases its bound iron. Iron-free 24p3 can withdraw iron from inside the cell to the outside by a reverse mechanism. We analyzed the role of the murine 24p3 gene Lcn2 (alias 24p3) as a target of the Wnt pathway. In cells with activated Wnt pathway, the levels of 24p3 protein and RNA were decreased. The withdrawal of iron led to 24p3 downregulation, and iron addition to iron-deprived cells induced 24p3 expression. Despite its strong inhibitory effect on 24p3 expression, Wnt pathway activation had no effect on the intracellular iron level. In cells with nonactivated Wnt pathway, we found an as yet unidentified transcript of 24p3R. Our results indicate independent regulation of 24p3 expression by the Wnt pathway and by the intracellular iron level. Differential splicing of the 24p3R transcript, depending on the activation state of the Wnt pathway, may modify the function of 24p3.
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Affiliation(s)
- Slava Ziegler
- Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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Ziegler S, Röhrs S, Tickenbrock L, Möröy T, Klein-Hitpass L, Vetter IR, Müller O. Novel target genes of the Wnt pathway and statistical insights into Wnt target promoter regulation. FEBS J 2005; 272:1600-15. [PMID: 15794748 DOI: 10.1111/j.1742-4658.2005.04581.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Wnt pathway controls biological processes via the regulation of target gene expression. The expression of direct Wnt target genes, e.g. cyclin D1 and MYC, is activated by the transcription factor TCF, which binds to specific sequence motifs in the promoter. Indirect target genes are regulated via transcription regulators, which are targets of the Wnt pathway. As an example, MYC regulates the MYC interacting zinc finger protein-1 (MIZ-1), which is able to inhibit the expression of the indirect target p21WAF1. We intended to identify new Wnt target genes and to get a deeper insight into the regulatory mechanisms of Wnt target gene expression. For this we analyzed the differential expression pattern of Wnt-1 activated cells by microarray analysis. We identified 43 sequences including eight expressed sequence tags (ESTs), which showed increased transcript levels, and 104 sequences including 19 ESTs with decreased RNA levels. Northern blot and real-time quantitative PCR analysis of the differential expression levels of 15 genes confirmed the differential expression trends of eight candidate genes. When the Wnt pathway was regulated at the lower level of glycogen synthase kinase-3 beta (GSK-3 beta) or adenomatous polyposis coli (APC), we detected discrepant expression trends. We compared the number of binding sites of transcription factors in the genomic regions of all candidate target genes with the number of sites in control genes. We found that the genomic regions of the down-regulated genes include an increased number of putative MIZ-1 binding sites. Our study introduces several new Wnt target genes and provides indications that the specific gene expression pattern depends on the type of the activation trigger or the level of interference with the Wnt pathway. Furthermore, our data indicate that a high proportion of Wnt target genes are regulated by indirect mechanisms.
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Affiliation(s)
- Slava Ziegler
- Max-Planck-Institut für molekulare Physiologie, Dortmund, Germany
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Magnusson C, Svensson A, Christerson U, Tågerud S. Denervation-induced alterations in gene expression in mouse skeletal muscle. Eur J Neurosci 2005; 21:577-80. [PMID: 15673457 DOI: 10.1111/j.1460-9568.2005.03855.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Motoneurons are important for regulating the function and properties of skeletal muscle. In the present study high-density oligonucleotide arrays have been used to compare gene expression in innervated and six-days denervated NMRI mouse skeletal muscle. To avoid looking at genes mainly participating in the process of atrophy, both hind-limb muscles (atrophic after denervation) and hemidiaphragm muscle (transiently hypertrophic after denervation) were used. Only genes previously not known to respond to denervation and with potential roles in DNA/RNA interactions/transcription and/or cellular communication/signalling are presented. Data for additional genes are provided as supplementary material. Thirty-two genes, up-regulated by a factor of two or down-regulated to the same extent after denervation, are presented. These include genes that may act through chromatin remodelling and/or as transcription factors/regulators (Cdkn1a, Cdr2, Hrmt1l2, Idb2, Myc/c-myc, L-myc1, Rb1, Sap30 and Tgif), genes possibly involved in the regulation of muscle membrane properties and/or excitation-contraction coupling (Cacng1, Camk2d, Hrmt1l2, Kcnj12, Kcna7 and Rrad) and genes potentially involved in neuromuscular interactions and/or receptor signalling (Acvr2b, Adam19, D0H4S114, Kai1, Maged1, Mt2, Prkcabp, Ptp4a3, Ramp1, Rras, Timp1, Vegfa and Zfp145). A set of five genes with altered expression after denervation (Fzd9, Nr4a1, Frat2, Ctgf and Cyr61) indicate that Wnt signalling may be reduced in denervated skeletal muscle.
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Affiliation(s)
- Caroline Magnusson
- Department of Chemistry and Biomedical Sciences, University of Kalmar, SE-391 82 Kalmar, Sweden
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Karaguni IM, Gourzoulidou E, Carpintero M, Langerak A, Klein-Hitpass L, Möröy T, Winde G, Waldmann H, Müller O. SMAF-1 Inhibits the APC/β-Catenin Pathway and Shows Properties Similar to Those of the Tumor Suppressor Protein APC. Chembiochem 2004; 5:1267-70. [PMID: 15368578 DOI: 10.1002/cbic.200400078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ioanna-Maria Karaguni
- Max-Planck-Institut für Molekulare Physiologie, Abteilung Strukturelle Biologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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