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Ineveld RL, Margaritis T, Kooiman BA, Groenveld F, Ariese HC, Lijnzaad P, Johnson HR, Korving J, Wehrens EJ, Holstege F, Rheenen J, Drost J, Rios AC, Bos FL. Cover Image. Dev Dyn 2021. [DOI: 10.1002/dvdy.432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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2
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Daub J, Amini S, Ma X, Jager N, Zhang J, Pfister S, Holstege F, Kemmeren P. Abstract 2235: A comprehensive map of genetic interactions in childhood cancer reveals multiple underlying biological mechanisms. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Despite increasing survival rates, childhood cancer is still the major cause of disease-related child death in developed countries. Genetic interactions between mutated genes play an important role in cancer development. They can be detected by searching for pairs of mutated genes that co-occur more (or less) often than expected. Co-occurrence suggests a cooperative role in cancer development, while mutual exclusivity points to synthetic lethality, a phenomenon of interest in cancer treatment research. Little is however known about genetic interactions in childhood cancer. Here, we apply a statistical pipeline to detect genetic interactions in a combined dataset comprising over 2,500 tumors from 23 cancer types. The resulting genetic interaction map of childhood cancers comprises 15 co-occurring and 27 mutually exclusive candidates. The biological mechanisms underlying most candidates are either tumor subtype, pathway epistasis or cooperation while synthetic lethality plays a much smaller role. Thus, other explanations beyond synthetic lethality should be considered when interpreting results of genetic interaction tests.
Citation Format: Josephine Daub, Saman Amini, Xiaotu Ma, Natalie Jager, Jinghui Zhang, Stefan Pfister, Frank Holstege, Patrick Kemmeren. A comprehensive map of genetic interactions in childhood cancer reveals multiple underlying biological mechanisms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2235.
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Affiliation(s)
- Josephine Daub
- 1Princess Maxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Saman Amini
- 1Princess Maxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Xiaotu Ma
- 2St Jude Children's Research Hospital, Memphis, TN
| | - Natalie Jager
- 3German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Stefan Pfister
- 3German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frank Holstege
- 1Princess Maxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Patrick Kemmeren
- 1Princess Maxima Center for Pediatric Oncology, Utrecht, Netherlands
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3
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van Ineveld RL, Margaritis T, Kooiman BAP, Groenveld F, Ariese HCR, Lijnzaad P, Johnson HR, Korving J, Wehrens EJ, Holstege F, van Rheenen J, Drost J, Rios AC, Bos FL. LGR6 marks nephron progenitor cells. Dev Dyn 2021; 250:1568-1583. [PMID: 33848015 PMCID: PMC8597161 DOI: 10.1002/dvdy.346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 11/12/2022] Open
Abstract
Background Nephron progenitor cells (NPCs) undergo a stepwise process to generate all mature nephron structures. Mesenchymal to epithelial transition (MET) is considered a multistep process of NPC differentiation to ensure progressive establishment of new nephrons. However, despite this important role, to date, no marker for NPCs undergoing MET in the nephron exists. Results Here, we identify LGR6 as a NPC marker, expressed in very early cap mesenchyme, pre‐tubular aggregates, renal vesicles, and in segments of S‐shaped bodies, following the trajectory of MET. By using a lineage tracing approach in embryonic explants in combination with confocal imaging and single‐cell RNA sequencing, we provide evidence for the multiple fates of LGR6+ cells during embryonic nephrogenesis. Moreover, by using long‐term in vivo lineage tracing, we show that postnatal LGR6+ cells are capable of generating the multiple lineages of the nephrons. Conclusions Given the profound early mesenchymal expression and MET signature of LGR6+ cells, together with the lineage tracing of mesenchymal LGR6+ cells, we conclude that LGR6+ cells contribute to all nephrogenic segments by undergoing MET. LGR6+ cells can therefore be considered an early committed NPC population during embryonic and postnatal nephrogenesis with potential regenerative capability. Lgr6 is expressed in the earliest cap mesenchyme pool, a niche where nephrogenic progenitor cells (NPCs) are found. Lgr6 marks NPCs undergoing mesenchymal to epithelial transition, following the main process of nephron development. Using ex vivo and vivo lineage tracing, we show that mesenchymal Lgr6 expressing cells give rise to multiple types of mesenchymal derived nephron segments, including specialized glomerular epithelium, such as podocytes.
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Affiliation(s)
- Ravian L van Ineveld
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | | | | | - Femke Groenveld
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Utrecht, The Netherlands
| | - Hendrikus C R Ariese
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Philip Lijnzaad
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Hannah R Johnson
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Jeroen Korving
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Utrecht, The Netherlands
| | - Ellen J Wehrens
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Frank Holstege
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Jacco van Rheenen
- Oncode Institute, Utrecht, The Netherlands.,Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Anne C Rios
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
| | - Frank L Bos
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Oncode Institute, Utrecht, The Netherlands
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Calandrini C, Schutgens F, Oka R, Margaritis T, Candelli T, Mathijsen L, Ammerlaan C, van Ineveld R, Derakhshan S, Custers L, Lijnzaad P, Begthel H, Kerstens H, Rookmaker M, Verhaar M, Kemmeren P, de Krijger R, Pritchard-Jones K, Rios A, van den Heuvel-Eibrink M, Holstege F, van Boxtel R, Clevers H, Drost J. Abstract IA27: Patient-derived organoids in pediatric cancer research. Cancer Res 2020. [DOI: 10.1158/1538-7445.pedca19-ia27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Recent advances in in vitro culture technologies, such as adult stem cell-derived organoids, have opened up new avenues for the development of novel, more physiologic human cancer models. Such preclinical models are essential for efficient translation of basic cancer research into novel treatment regimens. We succeeded in growing organoids from a range of pediatric solid tumors, including Wilms’ tumors, renal cell carcinomas, and different types of rhabdoid tumors (i.e., AT/RT, MRT). Tumor organoids retain many characteristics of parental tumor tissue. For instance, Wilms’ tumor organoids retain the cellular heterogeneity of tumors, as they are composed of an intricate network of different cell types. Moreover, we demonstrate that tumor organoids are amenable to gene editing and high-throughput drug screens. In conclusion, our pediatric cancer organoids capture disease and tissue heterogeneity and provide a platform for basic cancer research, drug screening, and personalized medicine.
Citation Format: Camilla Calandrini, Frans Schutgens, Rurika Oka, Thanasis Margaritis, Tito Candelli, Luka Mathijsen, Carola Ammerlaan, Ravian van Ineveld, Sepideh Derakhshan, Lars Custers, Philip Lijnzaad, Harry Begthel, Hinri Kerstens, Maarten Rookmaker, Marianne Verhaar, Patrick Kemmeren, Ronald de Krijger, Kathy Pritchard-Jones, Anne Rios, Marry van den Heuvel-Eibrink, Frank Holstege, Ruben van Boxtel, Hans Clevers, Jarno Drost. Patient-derived organoids in pediatric cancer research [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr IA27.
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Affiliation(s)
| | | | - Rurika Oka
- 1Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,
| | | | - Tito Candelli
- 1Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,
| | - Luka Mathijsen
- 1Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,
| | | | | | | | - Lars Custers
- 1Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,
| | - Philip Lijnzaad
- 1Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,
| | | | - Hinri Kerstens
- 1Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,
| | | | | | - Patrick Kemmeren
- 1Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,
| | - Ronald de Krijger
- 1Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,
| | | | - Anne Rios
- 1Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,
| | | | - Frank Holstege
- 1Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,
| | - Ruben van Boxtel
- 1Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,
| | | | - Jarno Drost
- 1Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,
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Charitou P, Rodriguez-Colman M, Gerrits J, van Triest M, Groot Koerkamp M, Hornsveld M, Holstege F, Verhoeven-Duif NM, Burgering BMT. FOXOs support the metabolic requirements of normal and tumor cells by promoting IDH1 expression. EMBO Rep 2015; 16:456-66. [PMID: 25648147 DOI: 10.15252/embr.201439096] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 01/08/2015] [Indexed: 01/02/2023] Open
Abstract
FOXO transcription factors are considered bona fide tumor suppressors; however, recent studies showed FOXOs are also required for tumor survival. Here, we identify FOXOs as transcriptional activators of IDH1. FOXOs promote IDH1 expression and thereby maintain the cytosolic levels of α-ketoglutarate and NADPH. In cancer cells carrying mutant IDH1, FOXOs likewise stimulate mutant IDH1 expression and maintain the levels of the oncometabolite 2-hydroxyglutarate, which stimulates cancer cell proliferation and inhibits TET enzymes and histone demethylases. Combined, our data provide a new paradigm for the paradoxical role of FOXOs in both tumor suppression and promotion.
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Affiliation(s)
- Paraskevi Charitou
- Department of Molecular Cancer Research, University Medical Center Utrecht, CG Utrecht, The Netherlands
| | - Maria Rodriguez-Colman
- Department of Molecular Cancer Research, University Medical Center Utrecht, CG Utrecht, The Netherlands
| | - Johan Gerrits
- Department of Medical Genetics, UMC Utrecht, Utrecht, The Netherlands
| | - Miranda van Triest
- Department of Molecular Cancer Research, University Medical Center Utrecht, CG Utrecht, The Netherlands
| | - Marian Groot Koerkamp
- Department of Molecular Cancer Research, University Medical Center Utrecht, CG Utrecht, The Netherlands
| | - Marten Hornsveld
- Department of Molecular Cancer Research, University Medical Center Utrecht, CG Utrecht, The Netherlands
| | - Frank Holstege
- Department of Molecular Cancer Research, University Medical Center Utrecht, CG Utrecht, The Netherlands
| | | | - Boudewijn M T Burgering
- Department of Molecular Cancer Research, University Medical Center Utrecht, CG Utrecht, The Netherlands
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6
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Leusink F, van Es R, de Bree R, de Jong RB, van Hooff S, Holstege F, Slootweg P, Brakenhoff R, Takes R. OP203. Oral Oncol 2013. [DOI: 10.1016/j.oraloncology.2013.03.212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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7
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Takes R, de Jong RB, Leusink F, van Hooff S, Kook R, van Diest P, Roepman P, van Velthuysen M, Merkx T, Jansen J, Schuuring E, Lacko M, de Herdt M, Slootweg P, Holstege F. MULTI-CENTER VALIDATION OF A LYMPH NODE METASTASIS GENE-EXPRESSION SIGNATURE FOR HEAD AND NECK SQUAMOUS CELL CARCINOMAS. Radiother Oncol 2011. [DOI: 10.1016/s0167-8140(11)70011-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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8
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Esnault C, Ghavi-Helm Y, Brun S, Soutourina J, Van Berkum N, Boschiero C, Holstege F, Werner M. Mediator-dependent recruitment of TFIIH modules in preinitiation complex. Mol Cell 2008; 31:337-46. [PMID: 18691966 DOI: 10.1016/j.molcel.2008.06.021] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2007] [Revised: 02/10/2008] [Accepted: 06/01/2008] [Indexed: 11/18/2022]
Abstract
In vitro, without Mediator, the association of general transcription factors (GTF) and RNA polymerase II (Pol II) in preinitiation complexes (PIC) occurs in an orderly fashion. In this work, we explore the in vivo function of Mediator in GTF recruitment to PIC. A direct interaction between Med11 Mediator head subunit and Rad3 TFIIH subunit was identified. We explored the significance of this interaction and those of Med11 with head module subunits Med17 and Med22 and found that impairing these interactions could differentially affect the recruitment of TFIIH, TFIIE, and Pol II in the PIC. A med11 mutation that altered promoter occupancy by the TFIIK kinase module of TFIIH genome-wide also reduced Pol II CTD serine 5 phosphorylation. We conclude that the Mediator head module plays a critical role in TFIIH and TFIIE recruitment to the PIC. We identify steps in PIC formation that suggest a branched assembly pathway.
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9
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Muller P, van Bakel H, van de Sluis B, Holstege F, Wijmenga C, Klomp LWJ. Gene expression profiling of liver cells after copper overload in vivo and in vitro reveals new copper-regulated genes. J Biol Inorg Chem 2007; 12:495-507. [PMID: 17211630 DOI: 10.1007/s00775-006-0201-y] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2006] [Accepted: 12/07/2006] [Indexed: 11/28/2022]
Abstract
Copper toxicity in the liver is mediated by free-radical generation, resulting in oxidative stress. To prevent toxic accumulation of copper, liver cells adapt to high copper levels. Here, we used microarray analysis to compare the adaptive responses on global gene expression in liver cells exposed to high copper levels in vitro and in vivo. In HepG2 cells we identified two clusters of upregulated genes over time, an "early" cluster that comprised metallothionein genes and a "late" cluster, highly enriched in genes involved in proteasomal degradation and in oxidative stress response. Concomitant with the "late" cluster, we detected a significant downregulation of several copper metabolism MURR1 domain (COMMD) genes that were recently implicated in copper metabolism and inhibition of nuclear transcription factor kappaB (NF-kappaB) signaling. As metal-induced oxidative stress increases NF-kappaB activity, our data suggest a role for reduced COMMD protein levels in prolonged activation of NF-kappaB, thus inducing cell survival. Mice exposed to a copper diet that highly exceeded normal daily intake accumulated only twofold more hepatic copper than control mice. Although a moderate, but significant upregulation of a set of 22 genes involved in immunity, iron and cholesterol metabolism was detected, these cannot account for direct mechanisms involved in copper excretion. In conclusion, we identified a novel set of genes that represent a delayed response to copper overload, thus providing insight into the adaptive transcriptional response to copper-induced oxidative stress.
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Affiliation(s)
- Patricia Muller
- Laboratory for Metabolic and Endocrine Diseases, University Medical Centre, Utrecht, The Netherlands
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10
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Birkenkamp KU, Essafi A, van der Vos KE, da Costa M, Hui RCY, Holstege F, Koenderman L, Lam EWF, Coffer PJ. FOXO3a induces differentiation of Bcr-Abl-transformed cells through transcriptional down-regulation of Id1. J Biol Chem 2006; 282:2211-20. [PMID: 17132628 DOI: 10.1074/jbc.m606669200] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Leukemic transformation often requires activation of protein kinase B (PKB/c-Akt) and is characterized by increased proliferation, decreased apoptosis, and a differentiation block. PKB phosphorylates and inactivates members of the FOXO subfamily of Forkhead transcription factors. It has been suggested that hyperactivation of PKB maintains the leukemic phenotype through actively repressing FOXO-mediated regulation of specific genes. We have found expression of the transcriptional repressor Id1 (inhibitor of DNA binding 1) to be abrogated by FOXO3a activation. Inhibition of PKB activation or growth factor deprivation also resulted in strong down-regulation of Id1 promoter activity, Id1 mRNA, and protein expression. Id1 is highly expressed in Bcr-Abl-transformed K562 cells, correlating with high PKB activation and FOXO3a phosphorylation. Inhibition of Bcr-Abl by the chemical inhibitor STI571 resulted in activation of FOXO3a and down-regulation of Id1 expression. By performing chromatin immunoprecipitation assays and promoter-mutation analysis, we demonstrate that FOXO3a acts as a transcriptional repressor by directly binding to the Id1 promoter. STI571 treatment, or expression of constitutively active FOXO3a, resulted in erythroid differentiation of K562 cells, which was inhibited by ectopic expression of Id1. Taken together our data strongly suggest that high expression of Id1, through PKB-mediated inhibition of FOXO3a, is critical for maintenance of the leukemic phenotype.
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Affiliation(s)
- Kim U Birkenkamp
- Molecular Immunology Laboratory, Department of Immunology, University Medical Center, KC.02.085.2, Lundiaan 6, 3584-CX Utrecht, The Netherlands
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Stoeckert C, Ball C, Brazma A, Brinkman R, Causton H, Fan L, Fostel J, Fragoso G, Heiskanen M, Holstege F, Morrison N, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, Sarkans U, Sherlock G, Stevens R, Taylor C, Taylor R, Whetzel P, White J. Wrestling with SUMO and bio-ontologies. Nat Biotechnol 2006; 24:21-2; author reply 23. [PMID: 16404382 DOI: 10.1038/nbt0106-21a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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12
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Hijnen D, Nijhuis E, Bruin-Weller M, Holstege F, Koerkamp MG, Kok I, Bruijnzeel-Koomen C, Knol E. Differential expression of genes involved in skin homing, proliferation, and apoptosis in CD4+ T cells of patients with atopic dermatitis. J Invest Dermatol 2006; 125:1149-55. [PMID: 16354184 DOI: 10.1111/j.0022-202x.2005.23932.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
CD4+ T cells play a critical role in allergic diseases, both in the affected tissue as well as systemically. Our objective was to investigate the in vivo activation state of peripheral blood CD4+ T cells of atopic dermatitis (AD) patients by analyzing gene expression profiles of unstimulated CD4+ T cells. mRNA samples from blood CD4+ T cells, isolated from five AD patients and seven healthy controls (HC), were analyzed using oligonucleotide arrays. Differentially regulated genes were validated by quantitative PCR (Q-PCR) in a larger group of patients with AD, in a group of patients with allergic asthma (AA), and HC subjects. In addition, "typical" T helper type 1 (Th1)- and Th2-related genes were analyzed by Q-PCR. Microarray analysis revealed differential expression of 52 genes in AD patients. Q-PCR confirmed several differentially regulated genes in AD, including CCR10, CRTH2, C-JUN, and NR4A2. Two groups of genes with highly correlating gene expression levels involved in tissue homing and proliferation or apoptosis, respectively, were identified. No marked differences were found in gene expression levels of typical Th1 or Th2 genes in AD or in AA patients. This study demonstrates that peripheral blood, unstimulated CD4+ T cells in AD patients show differentially expressed genes involved in tissue homing, proliferation, and apoptosis. No marked expression differences of "typical" atopy genes were found.
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Affiliation(s)
- Dirkjan Hijnen
- Department of Dermatology & Allergology, University Medical Centre Utrecht, Utrecht, The Netherlands.
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13
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Braam B, de Roos R, Bluyssen H, Kemmeren P, Holstege F, Joles JA, Koomans H. Nitric oxide-dependent and nitric oxide-independent transcriptional responses to high shear stress in endothelial cells. Hypertension 2005; 45:672-80. [PMID: 15699468 DOI: 10.1161/01.hyp.0000154683.33414.94] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Shear stress modulates gene expression in endothelial cells (ECs) partly through nitric oxide (NO), acting via enhanced cGMP formation by guanylyl cyclase (GC). We addressed non-cGMP-mediated transcriptional responses to shear stress in human umbilical ECs subjected to high-laminar shear stress (25 dyn/cm2; 150 minutes). RNA was isolated, reverse-transcribed, Cy3/5-labeled, and hybridized to 19 K human microarrays. High shear (n=6), high shear with 100 micromol/L L-NAME (n=3), and high shear with 10 micromol/L ODQ (GC inhibitor) in the perfusate (n=3) was compared with samples not subjected to flow. Among genes responding to high shear were HMOX1 (up) and PPARG (down). A high percentage of gene expression modulation by shear was absent during concomitant L-NAME or ODQ. Several transcriptional modulators were found (up: SOX5, SOX25, ZNF151, HOXD10; down: SOX11); a number of genes were regulated by shear and by shear with ODQ, but not regulated during L-NAME, indicating a nitric oxide synthase (NOS)-dependent, guanylyl cyclase (GC)-independent pathway. Several genes only responded to shear stress during L-NAME, others only responded to shear during ODQ. Upstream binding site analysis indicated shear stress and NO-dependent regulation of transcription via SOX5 and SOX9. Although NO importantly modulated the effect of shear stress on EC transcription, HMOX1 was consistently induced by shear stress, but not dependent on NOS or GC. Using bio-informatics software and databases, a promoter analysis identified SOX5 and SOX9 as potential, novel, shear-sensitive, and NO-dependent transcriptional regulators. The role of HMOX1 as a potential backup for NOS and the downstream role of SOXes should be explored.
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Affiliation(s)
- Branko Braam
- Department of Nephrology and Hypertension, University Medical Center, F03.226, P.O. Box 85500, 3508 GA Utrecht, The Netherlands.
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14
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Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ, Stewart JE, Taylor R, Brazma A, Quackenbush J. The underlying principles of scientific publication. Bioinformatics 2002; 18:1409. [PMID: 12424109 DOI: 10.1093/bioinformatics/18.11.1409] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15
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Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ, Stewart JE, Taylor R, Brazma A, Quackenbush J. Standards for microarray data. Science 2002; 298:539. [PMID: 12387284 DOI: 10.1126/science.298.5593.539b] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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16
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van de Wetering M, Oosterwegel M, Holstege F, Dooyes D, Suijkerbuijk R, Geurts van Kessel A, Clevers H. The human T cell transcription factor-1 gene. Structure, localization, and promoter characterization. J Biol Chem 1992; 267:8530-6. [PMID: 1569101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We have recently isolated cDNA clones representing four alternative splice forms of a T cell-specific transcription factor, TCF-1. Here we report the characterization of the human gene encoding this factor. The TCF-1 gene is contained in 10 exons including an untranslated first exon. The DNA-binding high mobility group (HMG) box of TCF-1 is encoded by the closely spaced exons VI and VII. Differential splicing involves an alternative exon (IX) and three splice acceptor sites in exon X. Based on comparison of sequence and on the placement of an alternative exon, TCF-1 appears closely related to the recently characterized HMG box transcription factor TCF-1 alpha/LEF. In particular, the HMG boxes encoded by the two TCF genes are virtually identical. The TCF-1 gene resides on chromosome 5 band q31.1. The TCF-1 promoter coincides with a CpG island. As determined by chloramphenicol acetyltransferase analysis, the promoter is preferentially active in T cells. The promoter does not contain TCF-1/TCF-1 alpha binding sites and is therefore not autoregulated. This observation implies the existence of yet uncharacterized T cell transcription factors that are active during early T cell differentiation.
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Affiliation(s)
- M van de Wetering
- Department of Clinical Immunology, University Hospital Utrecht, The Netherlands
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17
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van de Wetering M, Oosterwegel M, Holstege F, Dooyes D, Suijkerbuijk R, Geurts van Kessel A, Clevers H. The human T cell transcription factor-1 gene. Structure, localization, and promoter characterization. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)42476-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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