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Pontius WD, Hong ES, Faber ZJ, Gray J, Peacock CD, Bayles I, Lovrenert K, Chin DH, Gryder BE, Bartels CF, Scacheri PC. Temporal chromatin accessibility changes define transcriptional states essential for osteosarcoma metastasis. Nat Commun 2023; 14:7209. [PMID: 37938582 PMCID: PMC10632377 DOI: 10.1038/s41467-023-42656-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 10/17/2023] [Indexed: 11/09/2023] Open
Abstract
The metastasis-invasion cascade describes the series of steps required for a cancer cell to successfully spread from its primary tumor and ultimately grow within a secondary organ. Despite metastasis being a dynamic, multistep process, most omics studies to date have focused on comparing primary tumors to the metastatic deposits that define end-stage disease. This static approach means we lack information about the genomic and epigenomic changes that occur during the majority of tumor progression. One particularly understudied phase of tumor progression is metastatic colonization, during which cells must adapt to the new microenvironment of the secondary organ. Through temporal profiling of chromatin accessibility and gene expression in vivo, we identify dynamic changes in the epigenome that occur as osteosarcoma tumors form and grow within the lung microenvironment. Furthermore, we show through paired in vivo and in vitro CRISPR drop-out screens and pharmacological validation that the upstream transcription factors represent a class of metastasis-specific dependency genes. While current models depict lung colonization as a discrete step within the metastatic cascade, our study shows it is a defined trajectory through multiple epigenetic states, revealing new therapeutic opportunities undetectable with standard approaches.
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Affiliation(s)
- W Dean Pontius
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, USA.
| | - Ellen S Hong
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Zachary J Faber
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Jeremy Gray
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Craig D Peacock
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Ian Bayles
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Katreya Lovrenert
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Diana H Chin
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Berkley E Gryder
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Cynthia F Bartels
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
- Amgen Research, Discovery Biomarkers, Thousand Oaks, CA, USA.
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2
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Bayik D, Bartels CF, Lovrenert K, Watson DC, Zhang D, Kay K, Lee J, Lauko A, Johnson S, Lo A, Silver DJ, McGraw M, Grabowski M, Mohammadi AM, Veglia F, Fan Y, Vogelbaum MA, Scacheri P, Lathia JD. Correction: Distinct Cell Adhesion Signature Defines Glioblastoma Myeloid-Derived Suppressor Cell Subsets. Cancer Res 2023; 83:1757. [PMID: 37183658 PMCID: PMC10183804 DOI: 10.1158/0008-5472.can-23-0773] [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: 05/16/2023]
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3
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Qu DC, Neu D, Khawaja ZQ, Wang R, Bartels CF, Lovrenert K, Chan ER, Hill-Baskin AE, Scacheri PC, Berger NA. Epigenetic effects of high-fat diet on intestinal tumorigenesis in C57BL/6J- Apc Min/+ mice. J Transl Genet Genom 2023; 7:3-16. [PMID: 36817228 PMCID: PMC9937564 DOI: 10.20517/jtgg.2022.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Aim Obesity and obesogenic diets might partly accelerate cancer development through epigenetic mechanisms. To determine these early effects, we investigated the impact of three days of a high-fat diet on epigenomic and transcriptomic changes in Apc Min/+ murine intestinal epithelia. Method ChIP-Seq and RNA-Seq were performed on small intestinal epithelia of WT and Apc Min/+ male mice fed high-fat diet (HFD) or low-fat diet (LFD) for three days to identify genomic regions associated with differential H3K27ac levels as a marker of variant enhancer loci (VELs) as well as differentially expressed genes (DEGs). Results Regarding epigenetic and transcriptomic changes, diet type (LFD vs. HFD) showed a significant impact, and genotype (WT vs.Apc Min/+) showed a small impact. Compared to LFD, HFD resulted in 1306 gained VELs, 230 lost VELs, 133 upregulated genes, and 127 downregulated genes in WT mice, with 1056 gained VELs, 371 lost VELs, 222 upregulated genes, and 182 downregulated genes in Apc Min/+ mice. Compared to the WT genotype, the Apc Min/+ genotype resulted in zero changed VELs for either diet type group, 21 DEGs for LFD, and 48 DEGs for HFD. Most gained VELs, and upregulated genes were associated with lipid metabolic processes. Gained VELs were also associated with Wnt signaling. Downregulated genes were associated with antigen presentation and processing. Conclusion Three days of HFD-induced epigenomic and transcriptomic changes involving metabolic and immunologic pathways that may promote tumor growth in the genetically predisposed murine intestine without affecting key cancer signaling pathways.
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Affiliation(s)
- Dan C Qu
- Center for Science, Health and Society, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Devin Neu
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Zain Q Khawaja
- Center for Science, Health and Society, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Ruoyu Wang
- Center for Science, Health and Society, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Cynthia F Bartels
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Katreya Lovrenert
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Ernest R Chan
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Anne E Hill-Baskin
- Center for Science, Health and Society, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Nathan A Berger
- Center for Science, Health and Society, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
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4
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Bayik D, Bartels CF, Lovrenert K, Watson DC, Zhang D, Kay K, Lee J, Lauko A, Johnson S, Lo A, Silver DJ, McGraw M, Grabowski M, Mohammadi AM, Veglia F, Fan Y, Vogelbaum MA, Scacheri P, Lathia JD. Distinct Cell Adhesion Signature Defines Glioblastoma Myeloid-Derived Suppressor Cell Subsets. Cancer Res 2022; 82:4274-4287. [PMID: 36126163 PMCID: PMC9664137 DOI: 10.1158/0008-5472.can-21-3840] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 06/27/2022] [Accepted: 09/14/2022] [Indexed: 01/07/2023]
Abstract
In multiple types of cancer, an increased frequency in myeloid-derived suppressor cells (MDSC) is associated with worse outcomes and poor therapeutic response. In the glioblastoma (GBM) microenvironment, monocytic (m) MDSCs represent the predominant subset. However, the molecular basis of mMDSC enrichment in the tumor microenvironment compared with granulocytic (g) MDSCs has yet to be determined. Here we performed the first broad epigenetic profiling of MDSC subsets to define underlying cell-intrinsic differences in behavior and found that enhanced gene accessibility of cell adhesion programs in mMDSCs is linked to their tumor-accelerating ability in GBM models upon adoptive transfer. Mouse and human mMDSCs expressed higher levels of integrin β1 and dipeptidyl peptidase-4 (DPP-4) compared with gMDSCs as part of an enhanced cell adhesion signature. Integrin β1 blockade abrogated the tumor-promoting phenotype of mMDSCs and altered the immune profile in the tumor microenvironment, whereas treatment with a DPP-4 inhibitor extended survival in preclinical GBM models. Targeting DPP-4 in mMDSCs reduced pERK signaling and their migration towards tumor cells. These findings uncover a fundamental difference in the molecular basis of MDSC subsets and suggest that integrin β1 and DPP-4 represent putative immunotherapy targets to attenuate myeloid cell-driven immune suppression in GBM. SIGNIFICANCE Epigenetic profiling uncovers cell adhesion programming as a regulator of the tumor-promoting functions of monocytic myeloid-derived suppressor cells in glioblastoma, identifying therapeutic targets that modulate the immune response and suppress tumor growth.
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Affiliation(s)
- Defne Bayik
- Lerner Research Institute, Cleveland Clinic, Ohio
- Case Comprehensive Cancer Center, Cleveland, Ohio
| | - Cynthia F. Bartels
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Katreya Lovrenert
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Dionysios C. Watson
- Lerner Research Institute, Cleveland Clinic, Ohio
- Case Comprehensive Cancer Center, Cleveland, Ohio
- University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Duo Zhang
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kristen Kay
- Lerner Research Institute, Cleveland Clinic, Ohio
| | - Juyeun Lee
- Lerner Research Institute, Cleveland Clinic, Ohio
| | - Adam Lauko
- Lerner Research Institute, Cleveland Clinic, Ohio
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio
- Case Western Reserve University, Medical Science Training Program, Cleveland, Ohio
| | | | - Alice Lo
- Lerner Research Institute, Cleveland Clinic, Ohio
| | - Daniel J. Silver
- Lerner Research Institute, Cleveland Clinic, Ohio
- Case Comprehensive Cancer Center, Cleveland, Ohio
| | - Mary McGraw
- Rose Ella Burkhardt Brain Tumor Center, Cleveland Clinic, Ohio
| | | | | | - Filippo Veglia
- Department of Immunology, Moffitt Cancer Center, Tampa, Florida
| | - Yi Fan
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Peter Scacheri
- Case Comprehensive Cancer Center, Cleveland, Ohio
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Justin D. Lathia
- Lerner Research Institute, Cleveland Clinic, Ohio
- Case Comprehensive Cancer Center, Cleveland, Ohio
- Rose Ella Burkhardt Brain Tumor Center, Cleveland Clinic, Ohio
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5
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Allan KC, Hu LR, Scavuzzo MA, Morton AR, Gevorgyan AS, Cohn EF, Clayton BL, Bederman IR, Hung S, Bartels CF, Madhavan M, Tesar PJ. Non-canonical Targets of HIF1a Impair Oligodendrocyte Progenitor Cell Function. Cell Stem Cell 2021; 28:257-272.e11. [PMID: 33091368 PMCID: PMC7867598 DOI: 10.1016/j.stem.2020.09.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 08/19/2020] [Accepted: 09/29/2020] [Indexed: 12/25/2022]
Abstract
Mammalian cells respond to insufficient oxygen through transcriptional regulators called hypoxia-inducible factors (HIFs). Although transiently protective, prolonged HIF activity drives distinct pathological responses in different tissues. Using a model of chronic HIF1a accumulation in pluripotent-stem-cell-derived oligodendrocyte progenitors (OPCs), we demonstrate that HIF1a activates non-canonical targets to impair generation of oligodendrocytes from OPCs. HIF1a activated a unique set of genes in OPCs through interaction with the OPC-specific transcription factor OLIG2. Non-canonical targets, including Ascl2 and Dlx3, were sufficient to block differentiation through suppression of the oligodendrocyte regulator Sox10. Chemical screening revealed that inhibition of MEK/ERK signaling overcame the HIF1a-mediated block in oligodendrocyte generation by restoring Sox10 expression without affecting canonical HIF1a activity. MEK/ERK inhibition also drove oligodendrocyte formation in hypoxic regions of human oligocortical spheroids. This work defines mechanisms by which HIF1a impairs oligodendrocyte formation and establishes that cell-type-specific HIF1a targets perturb cell function in response to low oxygen.
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Affiliation(s)
- Kevin C. Allan
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Lucille R. Hu
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Marissa A. Scavuzzo
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Andrew R. Morton
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Artur S. Gevorgyan
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Erin F. Cohn
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Benjamin L.L. Clayton
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Ilya R. Bederman
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Stevephen Hung
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Cynthia F. Bartels
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Mayur Madhavan
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Paul J. Tesar
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA.,Lead Contact,Correspondence:
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6
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Lu L, Liu X, Huang WK, Giusti-Rodríguez P, Cui J, Zhang S, Xu W, Wen Z, Ma S, Rosen JD, Xu Z, Bartels CF, Kawaguchi R, Hu M, Scacheri PC, Rong Z, Li Y, Sullivan PF, Song H, Ming GL, Li Y, Jin F. Robust Hi-C Maps of Enhancer-Promoter Interactions Reveal the Function of Non-coding Genome in Neural Development and Diseases. Mol Cell 2020; 79:521-534.e15. [PMID: 32592681 DOI: 10.1016/j.molcel.2020.06.007] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 06/01/2020] [Accepted: 06/01/2020] [Indexed: 11/30/2022]
Abstract
Genome-wide mapping of chromatin interactions at high resolution remains experimentally and computationally challenging. Here we used a low-input "easy Hi-C" protocol to map the 3D genome architecture in human neurogenesis and brain tissues and also demonstrated that a rigorous Hi-C bias-correction pipeline (HiCorr) can significantly improve the sensitivity and robustness of Hi-C loop identification at sub-TAD level, especially the enhancer-promoter (E-P) interactions. We used HiCorr to compare the high-resolution maps of chromatin interactions from 10 tissue or cell types with a focus on neurogenesis and brain tissues. We found that dynamic chromatin loops are better hallmarks for cellular differentiation than compartment switching. HiCorr allowed direct observation of cell-type- and differentiation-specific E-P aggregates spanning large neighborhoods, suggesting a mechanism that stabilizes enhancer contacts during development. Interestingly, we concluded that Hi-C loop outperforms eQTL in explaining neurological GWAS results, revealing a unique value of high-resolution 3D genome maps in elucidating the disease etiology.
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Affiliation(s)
- Leina Lu
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Xiaoxiao Liu
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Wei-Kai Huang
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Program in Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Jian Cui
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Shanshan Zhang
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Wanying Xu
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Zhexing Wen
- Departments of Psychiatry and Behavioral Sciences, Cell Biology, and Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Shufeng Ma
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jonathan D Rosen
- Department of Biostatistics, Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Zheng Xu
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biostatistics, Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Cynthia F Bartels
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Riki Kawaguchi
- Department of Psychiatry and Neurology, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Zhili Rong
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China; Dermatology Hospital, Southern Medical University, Guangzhou, 510091, China
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biostatistics, Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Patrick F Sullivan
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Psychiatry, University of North Carolina, Chapel Hill, NC 27599, USA; Karolinska Institutet, Department of Medical Epidemiology and Biostatistics, Stockholm 171 77, Sweden
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Program in Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Yan Li
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; College of Graduate Studies, Cleveland State University, Cleveland, OH 44115, USA.
| | - Fulai Jin
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; Department of Computer and Data Sciences, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA.
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7
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Factor DC, Barbeau AM, Allan KC, Hu LR, Madhavan M, Hoang AT, Hazel KEA, Hall PA, Nisraiyya S, Najm FJ, Miller TE, Nevin ZS, Karl RT, Lima BR, Song Y, Sibert AG, Dhillon GK, Volsko C, Bartels CF, Adams DJ, Dutta R, Gallagher MD, Phu W, Kozlenkov A, Dracheva S, Scacheri PC, Tesar PJ, Corradin O. Cell Type-Specific Intralocus Interactions Reveal Oligodendrocyte Mechanisms in MS. Cell 2020; 181:382-395.e21. [PMID: 32246942 PMCID: PMC7426147 DOI: 10.1016/j.cell.2020.03.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 12/18/2019] [Accepted: 03/03/2020] [Indexed: 02/08/2023]
Abstract
Multiple sclerosis (MS) is an autoimmune disease characterized by attack on oligodendrocytes within the central nervous system (CNS). Despite widespread use of immunomodulatory therapies, patients may still face progressive disability because of failure of myelin regeneration and loss of neurons, suggesting additional cellular pathologies. Here, we describe a general approach for identifying specific cell types in which a disease allele exerts a pathogenic effect. Applying this approach to MS risk loci, we pinpoint likely pathogenic cell types for 70%. In addition to T cell loci, we unexpectedly identified myeloid- and CNS-specific risk loci, including two sites that dysregulate transcriptional pause release in oligodendrocytes. Functional studies demonstrated inhibition of transcriptional elongation is a dominant pathway blocking oligodendrocyte maturation. Furthermore, pause release factors are frequently dysregulated in MS brain tissue. These data implicate cell-intrinsic aberrations outside of the immune system and suggest new avenues for therapeutic development. VIDEO ABSTRACT.
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Affiliation(s)
- Daniel C Factor
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Anna M Barbeau
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Kevin C Allan
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Lucille R Hu
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Mayur Madhavan
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - An T Hoang
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Kathryn E A Hazel
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Parker A Hall
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sagar Nisraiyya
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Fadi J Najm
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Tyler E Miller
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Zachary S Nevin
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Robert T Karl
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Bruna R Lima
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Yanwei Song
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | - Gursimran K Dhillon
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Christina Volsko
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Cynthia F Bartels
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Drew J Adams
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Ranjan Dutta
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | | | - William Phu
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alexey Kozlenkov
- James J. Peters VA Medical Center, Bronx, NY 10468, USA; Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Stella Dracheva
- James J. Peters VA Medical Center, Bronx, NY 10468, USA; Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Paul J Tesar
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Olivia Corradin
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
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8
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Morton AR, Dogan-Artun N, Faber ZJ, MacLeod G, Bartels CF, Piazza MS, Allan KC, Mack SC, Wang X, Gimple RC, Wu Q, Rubin BP, Shetty S, Angers S, Dirks PB, Sallari RC, Lupien M, Rich JN, Scacheri PC. Functional Enhancers Shape Extrachromosomal Oncogene Amplifications. Cell 2019; 179:1330-1341.e13. [PMID: 31761532 DOI: 10.1016/j.cell.2019.10.039] [Citation(s) in RCA: 163] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 09/20/2019] [Accepted: 10/29/2019] [Indexed: 12/11/2022]
Abstract
Non-coding regions amplified beyond oncogene borders have largely been ignored. Using a computational approach, we find signatures of significant co-amplification of non-coding DNA beyond the boundaries of amplified oncogenes across five cancer types. In glioblastoma, EGFR is preferentially co-amplified with its two endogenous enhancer elements active in the cell type of origin. These regulatory elements, their contacts, and their contribution to cell fitness are preserved on high-level circular extrachromosomal DNA amplifications. Interrogating the locus with a CRISPR interference screening approach reveals a diversity of additional elements that impact cell fitness. The pattern of fitness dependencies mirrors the rearrangement of regulatory elements and accompanying rewiring of the chromatin topology on the extrachromosomal amplicon. Our studies indicate that oncogene amplifications are shaped by regulatory dependencies in the non-coding genome.
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Affiliation(s)
- Andrew R Morton
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
| | - Nergiz Dogan-Artun
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Zachary J Faber
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
| | - Graham MacLeod
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Cynthia F Bartels
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
| | - Megan S Piazza
- Center for Human Genetics Laboratory, University Hospitals, Cleveland, OH 44106, USA
| | - Kevin C Allan
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
| | - Stephen C Mack
- Department of Pediatrics, Division of Hematology and Oncology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX 77030, USA
| | - Xiuxing Wang
- Department of Medicine, Division of Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Ryan C Gimple
- Department of Medicine, Division of Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Department of Pathology, Case Western Reserve University, Cleveland, OH 44120, USA
| | - Qiulian Wu
- Department of Medicine, Division of Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Brian P Rubin
- Departments of Anatomic Pathology and Molecular Genetics, Cleveland Clinic, Lerner Research Institute and Taussig Cancer Center, Cleveland, OH 44195, USA
| | - Shashirekha Shetty
- Center for Human Genetics Laboratory, University Hospitals, Cleveland, OH 44106, USA
| | - Stephane Angers
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada; Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, ON M5G 0A4, Canada
| | - Peter B Dirks
- Developmental and Stem Cell Biology Program and Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | | | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jeremy N Rich
- Department of Medicine, Division of Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Department of Neurosciences, University of California, San Diego, School of Medicine, La Jolla, CA 92037, USA.
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA.
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9
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Hung S, Saiakhova A, Faber ZJ, Bartels CF, Neu D, Bayles I, Ojo E, Hong ES, Pontius WD, Morton AR, Liu R, Kalady MF, Wald DN, Markowitz S, Scacheri PC. Mismatch repair-signature mutations activate gene enhancers across human colorectal cancer epigenomes. eLife 2019; 8:40760. [PMID: 30759065 PMCID: PMC6374075 DOI: 10.7554/elife.40760] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 08/03/2018] [Accepted: 01/22/2019] [Indexed: 02/07/2023] Open
Abstract
Commonly-mutated genes have been found for many cancers, but less is known about mutations in cis-regulatory elements. We leverage gains in tumor-specific enhancer activity, coupled with allele-biased mutation detection from H3K27ac ChIP-seq data, to pinpoint potential enhancer-activating mutations in colorectal cancer (CRC). Analysis of a genetically-diverse cohort of CRC specimens revealed that microsatellite instable (MSI) samples have a high indel rate within active enhancers. Enhancers with indels show evidence of positive selection, increased target gene expression, and a subset is highly recurrent. The indels affect short homopolymer tracts of A/T and increase affinity for FOX transcription factors. We further demonstrate that signature mismatch-repair (MMR) mutations activate enhancers using a xenograft tumor metastasis model, where mutations are induced naturally via CRISPR/Cas9 inactivation of MLH1 prior to tumor cell injection. Our results suggest that MMR signature mutations activate enhancers in CRC tumor epigenomes to provide a selective advantage.
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Affiliation(s)
- Stevephen Hung
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States
| | - Alina Saiakhova
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States
| | - Zachary J Faber
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States
| | - Cynthia F Bartels
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States
| | - Devin Neu
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States
| | - Ian Bayles
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States
| | - Evelyn Ojo
- Department of Pathology, Case Western Reserve University, Cleveland, United States
| | - Ellen S Hong
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States
| | - W Dean Pontius
- Department of Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
| | - Andrew R Morton
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States
| | - Ruifu Liu
- Department of Pathology, Case Western Reserve University, Cleveland, United States
| | - Matthew F Kalady
- Department of Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, United States.,Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, United States.,Department of Colorectal Surgery, Digestive Disease and Surgery Institute, Cleveland Clinic, Cleveland, United States
| | - David N Wald
- Department of Pathology, Case Western Reserve University, Cleveland, United States.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, United States
| | - Sanford Markowitz
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, United States.,Department of Medicine, Case Western Reserve University, Cleveland, United States
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, United States.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, United States
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10
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Yao H, Hill SF, Skidmore JM, Sperry ED, Swiderski DL, Sanchez GJ, Bartels CF, Raphael Y, Scacheri PC, Iwase S, Martin DM. CHD7 represses the retinoic acid synthesis enzyme ALDH1A3 during inner ear development. JCI Insight 2018; 3:97440. [PMID: 29467333 DOI: 10.1172/jci.insight.97440] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 01/23/2018] [Indexed: 12/13/2022] Open
Abstract
CHD7, an ATP-dependent chromatin remodeler, is disrupted in CHARGE syndrome, an autosomal dominant disorder characterized by variably penetrant abnormalities in craniofacial, cardiac, and nervous system tissues. The inner ear is uniquely sensitive to CHD7 levels and is the most commonly affected organ in individuals with CHARGE. Interestingly, upregulation or downregulation of retinoic acid (RA) signaling during embryogenesis also leads to developmental defects similar to those in CHARGE syndrome, suggesting that CHD7 and RA may have common target genes or signaling pathways. Here, we tested three separate potential mechanisms for CHD7 and RA interaction: (a) direct binding of CHD7 with RA receptors, (b) regulation of CHD7 levels by RA, and (c) CHD7 binding and regulation of RA-related genes. We show that CHD7 directly regulates expression of Aldh1a3, the gene encoding the RA synthetic enzyme ALDH1A3 and that loss of Aldh1a3 partially rescues Chd7 mutant mouse inner ear defects. Together, these studies indicate that ALDH1A3 acts with CHD7 in a common genetic pathway to regulate inner ear development, providing insights into how CHD7 and RA regulate gene expression and morphogenesis in the developing embryo.
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Affiliation(s)
- Hui Yao
- Department of Pediatrics and Communicable Diseases
| | | | | | - Ethan D Sperry
- Department of Human Genetics.,Medical Scientist Training Program, and
| | - Donald L Swiderski
- Department of Otolaryngology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Cynthia F Bartels
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio, USA
| | - Yehoash Raphael
- Department of Otolaryngology, University of Michigan, Ann Arbor, Michigan, USA
| | - Peter C Scacheri
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio, USA
| | | | - Donna M Martin
- Department of Pediatrics and Communicable Diseases.,Department of Human Genetics.,Medical Scientist Training Program, and
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11
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Morrow JJ, Bayles I, Funnell APW, Miller TE, Saiakhova A, Lizardo MM, Bartels CF, Kapteijn MY, Hung S, Mendoza A, Dhillon G, Chee DR, Myers JT, Allen F, Gambarotti M, Righi A, DiFeo A, Rubin BP, Huang AY, Meltzer PS, Helman LJ, Picci P, Versteeg H, Stamatoyannopolus J, Khanna C, Scacheri PC. Positively selected enhancer elements endow osteosarcoma cells with metastatic competence. Nat Med 2018; 24:176-185. [PMID: 29334376 PMCID: PMC5803371 DOI: 10.1038/nm.4475] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 12/18/2017] [Indexed: 12/13/2022]
Abstract
Metastasis results from a complex set of traits acquired by tumor cells, distinct from those necessary for tumorigenesis. Here, we investigate the contribution of enhancer elements to the metastatic phenotype of osteosarcoma. Through epigenomic profiling, we identify substantial differences in enhancer activity between primary and metastatic human tumors and between near isogenic pairs of highly lung metastatic and nonmetastatic osteosarcoma cell lines. We term these regions metastatic variant enhancer loci (Met-VELs). Met-VELs drive coordinated waves of gene expression during metastatic colonization of the lung. Met-VELs cluster nonrandomly in the genome, indicating that activity of these enhancers and expression of their associated gene targets are positively selected. As evidence of this causal association, osteosarcoma lung metastasis is inhibited by global interruptions of Met-VEL-associated gene expression via pharmacologic BET inhibition, by knockdown of AP-1 transcription factors that occupy Met-VELs, and by knockdown or functional inhibition of individual genes activated by Met-VELs, such as that encoding coagulation factor III/tissue factor (F3). We further show that genetic deletion of a single Met-VEL at the F3 locus blocks metastatic cell outgrowth in the lung. These findings indicate that Met-VELs and the genes they regulate play a functional role in metastasis and may be suitable targets for antimetastatic therapies.
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Affiliation(s)
- James J. Morrow
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ian Bayles
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | - Tyler E. Miller
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Alina Saiakhova
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Michael M. Lizardo
- Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892 USA
| | - Cynthia F. Bartels
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Maaike Y. Kapteijn
- Thrombosis and Hemostasis Division, Department of Internal Medicine, LUMC, Leiden, Netherlands
| | - Stevephen Hung
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Arnulfo Mendoza
- Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892 USA
| | - Gursimran Dhillon
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Daniel R. Chee
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Jay T. Myers
- Department of Pediatrics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Frederick Allen
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Marco Gambarotti
- Research Laboratory, Istituto Ortopedico Rizzoli, Via Pupilli 1, 40136, Bologna, Italy
| | - Alberto Righi
- Research Laboratory, Istituto Ortopedico Rizzoli, Via Pupilli 1, 40136, Bologna, Italy
| | - Analisa DiFeo
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Brian P. Rubin
- Departments of Anatomic Pathology and Molecular Genetics, Cleveland Clinic, Lerner Research Institute and Taussig Cancer Center, Cleveland, OH 44195, USA
| | - Alex Y. Huang
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Pediatrics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Paul S. Meltzer
- Genetics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892 USA
| | - Lee J. Helman
- Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892 USA
| | - Piero Picci
- Research Laboratory, Istituto Ortopedico Rizzoli, Via Pupilli 1, 40136, Bologna, Italy
| | - Henri Versteeg
- Thrombosis and Hemostasis Division, Department of Internal Medicine, LUMC, Leiden, Netherlands
| | | | - Chand Khanna
- Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892 USA
| | - Peter C. Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
- Research Laboratory, Istituto Ortopedico Rizzoli, Via Pupilli 1, 40136, Bologna, Italy
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12
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Merry CR, McMahon S, Forrest ME, Bartels CF, Saiakhova A, Bartel CA, Scacheri PC, Thompson CL, Jackson MW, Harris LN, Khalil AM. Transcriptome-wide identification of mRNAs and lincRNAs associated with trastuzumab-resistance in HER2-positive breast cancer. Oncotarget 2018; 7:53230-53244. [PMID: 27449296 PMCID: PMC5288181 DOI: 10.18632/oncotarget.10637] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 03/11/2016] [Accepted: 07/09/2016] [Indexed: 01/03/2023] Open
Abstract
Approximately, 25–30% of early-stage breast tumors are classified at the molecular level as HER2-positive, which is an aggressive subtype of breast cancer. Amplification of the HER2 gene in these tumors results in a substantial increase in HER2 mRNA levels, and consequently, HER2 protein levels. HER2, a transmembrane receptor tyrosine kinase (RTK), is targeted therapeutically by a monoclonal antibody, trastuzumab (Tz), which has dramatically improved the prognosis of HER2-driven breast cancers. However, ~30% of patients develop resistance to trastuzumab and recur; and nearly all patients with advanced disease develop resistance over time and succumb to the disease. Mechanisms of trastuzumab resistance (TzR) are not well understood, although some studies suggest that growth factor signaling through other receptors may be responsible. However, these studies were based on cell culture models of the disease, and thus, it is not known which pathways are driving the resistance in vivo. Using an integrative transcriptomic approach of RNA isolated from trastuzumab-sensitive and trastuzumab-resistant HER2+ tumors, and isogenic cell culture models, we identified a small set of mRNAs and lincRNAs that are associated with trastuzumab-resistance (TzR). Functional analysis of a top candidate gene, S100P, demonstrated that inhibition of S100P results in reversing TzR. Mechanistically, S100P activates the RAS/MEK/MAPK pathway to compensate for HER2 inhibition by trastuzumab. Finally, we demonstrated that the upregulation of S100P appears to be driven by epigenomic changes at the enhancer level. Our current findings should pave the path toward new therapies for breast cancer patients.
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Affiliation(s)
- Callie R Merry
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA.,Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Sarah McMahon
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Megan E Forrest
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Cynthia F Bartels
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Alina Saiakhova
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Courtney A Bartel
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Cheryl L Thompson
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA.,Department of Nutrition, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Mark W Jackson
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Lyndsay N Harris
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA.,Department of Medicine and Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ahmad M Khalil
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA.,Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
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13
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Cohen AJ, Saiakhova A, Corradin O, Luppino JM, Lovrenert K, Bartels CF, Morrow JJ, Mack SC, Dhillon G, Beard L, Myeroff L, Kalady MF, Willis J, Bradner JE, Keri RA, Berger NA, Pruett-Miller SM, Markowitz SD, Scacheri PC. Hotspots of aberrant enhancer activity punctuate the colorectal cancer epigenome. Nat Commun 2017; 8:14400. [PMID: 28169291 PMCID: PMC5309719 DOI: 10.1038/ncomms14400] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 12/22/2016] [Indexed: 12/12/2022] Open
Abstract
In addition to mutations in genes, aberrant enhancer element activity at non-coding regions of the genome is a key driver of tumorigenesis. Here, we perform epigenomic enhancer profiling of a cohort of more than forty genetically diverse human colorectal cancer (CRC) specimens. Using normal colonic crypt epithelium as a comparator, we identify enhancers with recurrently gained or lost activity across CRC specimens. Of the enhancers highly recurrently activated in CRC, most are constituents of super enhancers, are occupied by AP-1 and cohesin complex members, and originate from primed chromatin. Many activate known oncogenes, and CRC growth can be mitigated through pharmacologic inhibition or genome editing of these loci. Nearly half of all GWAS CRC risk loci co-localize to recurrently activated enhancers. These findings indicate that the CRC epigenome is defined by highly recurrent epigenetic alterations at enhancers which activate a common, aberrant transcriptional programme critical for CRC growth and survival.
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Affiliation(s)
- Andrea J. Cohen
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, Ohio 44106, USA
| | - Alina Saiakhova
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, Ohio 44106, USA
| | - Olivia Corradin
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, Ohio 44106, USA
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Jennifer M. Luppino
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, Ohio 44106, USA
| | - Katreya Lovrenert
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, Ohio 44106, USA
| | - Cynthia F. Bartels
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, Ohio 44106, USA
| | - James J. Morrow
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, Ohio 44106, USA
- Department of Pathology, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, Ohio 44106, USA
| | - Stephen C. Mack
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Ave, Cleveland, Ohio 44195, USA
| | - Gursimran Dhillon
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, Ohio 44106, USA
| | - Lydia Beard
- Case Comprehensive Cancer Center, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio 44106, USA
| | - Lois Myeroff
- Case Comprehensive Cancer Center, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio 44106, USA
| | - Matthew F. Kalady
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Ave, Cleveland, Ohio 44195, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio 44106, USA
- Department of Colorectal Surgery, Cleveland Clinic Foundation, 9500 Euclid Ave, Cleveland, Ohio 44195, USA
| | - Joseph Willis
- Department of Pathology, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, Ohio 44106, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio 44106, USA
- Department of Medicine, University Hospitals Cleveland Medical Center, 11100 Euclid Ave, Cleveland, Ohio 44106, USA
| | - James E. Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, Massachusetts 02215, USA
- Department of Medicine, Harvard Medical School, 25 Shattuck St, Boston, Massachusetts 02115, USA
| | - Ruth A. Keri
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, Ohio 44106, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio 44106, USA
- Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, Ohio 44106, USA
| | - Nathan A. Berger
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, Ohio 44106, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio 44106, USA
- Department of Medicine, University Hospitals Cleveland Medical Center, 11100 Euclid Ave, Cleveland, Ohio 44106, USA
| | - Shondra M. Pruett-Miller
- Genome Engineering and iPSC Center, Department of Genetics, Washington University, 4515 McKinley Building, St. Louis, Missouri 63110, USA
| | - Sanford D. Markowitz
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, Ohio 44106, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio 44106, USA
- Department of Medicine, University Hospitals Cleveland Medical Center, 11100 Euclid Ave, Cleveland, Ohio 44106, USA
| | - Peter C. Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, Ohio 44106, USA
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Ave, Cleveland, Ohio 44195, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio 44106, USA
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14
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Morrow JJ, Miller TE, Saiakhova A, Lizardo MM, Bartels CF, Bayles I, Hung S, Mendoza A, Myers JT, Allen F, DiFeo A, Rubin BP, Huang AY, Meltzer PS, Helman LJ, Khanna C, Scacheri PC. Abstract LB-151: Positively selected enhancer elements endow tumor cells with metastatic competence. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-lb-151] [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
Metastasis results from a complex set of traits acquired by tumor cells, distinct from those necessary for tumorigenesis. Here, we investigate the contribution of enhancer elements to the metastatic phenotype of osteosarcoma. Through epigenomic profiling, we identify substantial differences in signature enhancer-histone marks between near-isogenic pairs of high and low lung-metastatic osteosarcoma cells. We term these regions Metastatic Variant Enhancer Loci (Met-VELs). Met-VELs drive coordinated waves of gene expression during metastatic colonization of the lung. Met-VELs cluster non-randomly, indicating that activity of these enhancers and their associated gene targets is positively selected. Osteosarcoma lung metastasis is inhibited by global interruptions of Met-VEL associated gene expression via pharmacologic BET inhibition, by knockdown of AP-1 transcription factors whose motifs are enriched in Met-VELs, and by knockdown of individual genes activated by Met-VELs. These observations have implications for the discovery and development of targeted anti-metastatic therapies.
Citation Format: James J. Morrow, Tyler E. Miller, Alina Saiakhova, Michael M. Lizardo, Cynthia F. Bartels, Ian Bayles, Stevephen Hung, Arnulfo Mendoza, Jay T. Myers, Frederick Allen, Analisa DiFeo, Brian P. Rubin, Alex Y. Huang, Paul S. Meltzer, Lee J. Helman, Chand Khanna, Peter C. Scacheri. Positively selected enhancer elements endow tumor cells with metastatic competence. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-151.
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Affiliation(s)
- James J. Morrow
- 1Case Western Reserve University School of Medicine, Cleveland, OH
| | - Tyler E. Miller
- 1Case Western Reserve University School of Medicine, Cleveland, OH
| | - Alina Saiakhova
- 1Case Western Reserve University School of Medicine, Cleveland, OH
| | | | | | - Ian Bayles
- 1Case Western Reserve University School of Medicine, Cleveland, OH
| | - Stevephen Hung
- 1Case Western Reserve University School of Medicine, Cleveland, OH
| | | | - Jay T. Myers
- 1Case Western Reserve University School of Medicine, Cleveland, OH
| | - Frederick Allen
- 1Case Western Reserve University School of Medicine, Cleveland, OH
| | - Analisa DiFeo
- 1Case Western Reserve University School of Medicine, Cleveland, OH
| | - Brian P. Rubin
- 3Cleveland Clinic, Lerner Research Institute and Taussig Cancer Center, Cleveland, OH
| | - Alex Y. Huang
- 1Case Western Reserve University School of Medicine, Cleveland, OH
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15
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Bükülmez H, Khan F, Bartels CF, Murakami S, Ortiz-Lopez A, Sattar A, Haqqi TM, Warman ML. Protective effects of C-type natriuretic peptide on linear growth and articular cartilage integrity in a mouse model of inflammatory arthritis. Arthritis Rheumatol 2014; 66:78-89. [PMID: 24449577 PMCID: PMC4034591 DOI: 10.1002/art.38199] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 09/15/2013] [Indexed: 01/15/2023]
Abstract
Objective The C-type natriuretic peptide (CNP) signaling pathway is a major contributor to postnatal skeletal growth in humans. This study was undertaken to investigate whether CNP signaling could prevent growth delay and cartilage damage in an animal model of inflammatory arthritis. Methods We generated transgenic mice that overexpress CNP (B6.SJL-Col2a1-NPPC) in chondrocytes. We introduced the CNP transgene into mice with experimental systemic inflammatory arthritis (K/BxN T cell receptor [TCR]) and determined the effect of CNP overexpression in chondrocytes on the severity of arthritis, cartilage damage, and linear growth. We also examined primary chondrocyte cultures for changes in gene and protein expression resulting from CNP overexpression. Results K/BxN TCR mice exhibited linear growth delay (P < 0.01) compared to controls, and this growth delay was correlated with the severity of arthritis. Diminished chondrocyte proliferation and matrix production was also seen in K/BxN TCR mice. Compared to non–CNP-transgenic mice, K/BxN TCR mice with overexpressed CNP had milder arthritis, no growth delay, and less cartilage damage. Primary chondrocytes from mice overexpressing CNP were less sensitive to inflammatory cytokines than wild-type mouse chondrocytes. Conclusion CNP overexpression in chondrocytes can prevent endochondral growth delay and protect against cartilage damage in a mouse model of inflammatory arthritis. Pharmacologic or biologic modulation of the CNP signaling pathway may prevent growth retardation and protect cartilage in patients with inflammatory joint diseases, such as juvenile idiopathic arthritis.
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Affiliation(s)
- Hülya Bükülmez
- MetroHealth Medical Center and Case Western Reserve University, Cleveland, Ohio
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16
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Garcia Segarra N, Mittaz L, Campos-Xavier AB, Bartels CF, Tuysuz B, Alanay Y, Cimaz R, Cormier-Daire V, Di Rocco M, Duba HC, Elcioglu NH, Forzano F, Hospach T, Kilic E, Kuemmerle-Deschner JB, Mortier G, Mrusek S, Nampoothiri S, Obersztyn E, Pauli RM, Selicorni A, Tenconi R, Unger S, Utine GE, Wright M, Zabel B, Warman ML, Superti-Furga A, Bonafé L. The diagnostic challenge of progressive pseudorheumatoid dysplasia (PPRD): A review of clinical features, radiographic features, and WISP3 mutations in 63 affected individuals. Am J Med Genet 2012; 160C:217-29. [DOI: 10.1002/ajmg.c.31333] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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17
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Bukulmez H, Bartels CF, Nanda K, Haqqi TM, Welter JF. Cartilage-protective effects of C-type natriuretic peptide over expression in K/BxN TCR arthritis model. Pediatr Rheumatol Online J 2012. [PMCID: PMC3403025 DOI: 10.1186/1546-0096-10-s1-a109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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18
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Balasubramanian D, Akhtar-Zaidi B, Song L, Bartels CF, Veigl M, Beard L, Myeroff L, Guda K, Lutterbaugh J, Willis J, Crawford GE, Markowitz SD, Scacheri PC. H3K4me3 inversely correlates with DNA methylation at a large class of non-CpG-island-containing start sites. Genome Med 2012; 4:47. [PMID: 22640407 PMCID: PMC3506913 DOI: 10.1186/gm346] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 04/13/2012] [Accepted: 05/28/2012] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND In addition to mutations, epigenetic silencing of genes has been recognized as a fundamental mechanism that promotes human carcinogenesis. To date, characterization of epigenetic gene silencing has largely focused on genes in which silencing is mediated by hypermethylation of promoter-associated CpG islands, associated with loss of the H3K4me3 chromatin mark. Far less is known about promoters lacking CpG-islands or genes that are repressed by alternative mechanisms. METHODS We performed integrative ChIP-chip, DNase-seq, and global gene expression analyses in colon cancer cells and normal colon mucosa to characterize chromatin features of both CpG-rich and CpG-poor promoters of genes that undergo silencing in colon cancer. RESULTS Epigenetically repressed genes in colon cancer separate into two classes based on retention or loss of H3K4me3 at transcription start sites. Quantitatively, of transcriptionally repressed genes that lose H3K4me3 in colon cancer (K4-dependent genes), a large fraction actually lacks CpG islands. Nonetheless, similar to CpG-island containing genes, cytosines located near the start sites of K4-dependent genes become DNA hypermethylated, and repressed K4-dependent genes can be reactivated with 5-azacytidine. Moreover, we also show that when the H3K4me3 mark is retained, silencing of CpG island-associated genes can proceed through an alternative mechanism in which repressive chromatin marks are recruited. CONCLUSIONS H3K4me3 equally protects from DNA methylation at both CpG-island and non-CpG island start sites in colon cancer. Moreover, the results suggest that CpG-rich genes repressed by loss of H3K4me3 and DNA methylation represent special instances of a more general epigenetic mechanism of gene silencing, one in which gene silencing is mediated by loss of H3K4me3 and methylation of non-CpG island promoter-associated cytosines.
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Affiliation(s)
- Dheepa Balasubramanian
- Department of Genetics and Genome Sciences, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
| | - Batool Akhtar-Zaidi
- Department of Genetics and Genome Sciences, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, 9500 Euclid Ave, Cleveland, OH 44195, USA
| | - Lingyun Song
- Institute for Science and Policy, and Department of Pediatrics, Duke University, 101 Science Drive, Durham, NC 27708, USA
| | - Cynthia F Bartels
- Department of Genetics and Genome Sciences, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
| | - Martina Veigl
- Case Comprehensive Cancer Center, Case Western Reserve University, 11100 Euclid Ave, Cleveland, OH 44106, USA
| | - Lydia Beard
- Case Comprehensive Cancer Center, Case Western Reserve University, 11100 Euclid Ave, Cleveland, OH 44106, USA
| | - Lois Myeroff
- Case Comprehensive Cancer Center, Case Western Reserve University, 11100 Euclid Ave, Cleveland, OH 44106, USA
| | - Kishore Guda
- Case Comprehensive Cancer Center, Case Western Reserve University, 11100 Euclid Ave, Cleveland, OH 44106, USA
| | - James Lutterbaugh
- Case Comprehensive Cancer Center, Case Western Reserve University, 11100 Euclid Ave, Cleveland, OH 44106, USA
| | - Joseph Willis
- Case Comprehensive Cancer Center, Case Western Reserve University, 11100 Euclid Ave, Cleveland, OH 44106, USA
- Department of Pathology, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA
| | - Gregory E Crawford
- Institute for Science and Policy, and Department of Pediatrics, Duke University, 101 Science Drive, Durham, NC 27708, USA
| | - Sanford D Markowitz
- Department of Genetics and Genome Sciences, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, 11100 Euclid Ave, Cleveland, OH 44106, USA
- Department of Medicine, Case Western Reserve University, 10900 Euclid Ave Cleveland, OH 44106, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, 9500 Euclid Ave, Cleveland, OH 44195, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, 11100 Euclid Ave, Cleveland, OH 44106, USA
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Akhtar-Zaidi B, Cowper-Sal·lari R, Corradin O, Saiakhova A, Bartels CF, Balasubramanian D, Myeroff L, Lutterbaugh J, Jarrar A, Kalady MF, Willis J, Moore JH, Tesar PJ, Laframboise T, Markowitz S, Lupien M, Scacheri PC. Epigenomic enhancer profiling defines a signature of colon cancer. Science 2012; 336:736-9. [PMID: 22499810 PMCID: PMC3711120 DOI: 10.1126/science.1217277] [Citation(s) in RCA: 255] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cancer is characterized by gene expression aberrations. Studies have largely focused on coding sequences and promoters, even though distal regulatory elements play a central role in controlling transcription patterns. We used the histone mark H3K4me1 to analyze gain and loss of enhancer activity genome-wide in primary colon cancer lines relative to normal colon crypts. We identified thousands of variant enhancer loci (VELs) that comprise a signature that is robustly predictive of the in vivo colon cancer transcriptome. Furthermore, VELs are enriched in haplotype blocks containing colon cancer genetic risk variants, implicating these genomic regions in colon cancer pathogenesis. We propose that reproducible changes in the epigenome at enhancer elements drive a specific transcriptional program to promote colon carcinogenesis.
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Affiliation(s)
- Batool Akhtar-Zaidi
- Department of Genetics, Case Western Reserve University, Cleveland, OH 44106
| | - Richard Cowper-Sal·lari
- Norris Cotton Cancer Center, Institute for Quantitative Biomedical Sciences, Department of Genetics, Dartmouth Medical School, Lebanon, NH 03756, USA
| | - Olivia Corradin
- Department of Genetics, Case Western Reserve University, Cleveland, OH 44106
| | - Alina Saiakhova
- Department of Genetics, Case Western Reserve University, Cleveland, OH 44106
| | - Cynthia F. Bartels
- Department of Genetics, Case Western Reserve University, Cleveland, OH 44106
| | | | - Lois Myeroff
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - James Lutterbaugh
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Awad Jarrar
- Department of Colorectal Surgery, Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA
| | - Matthew F. Kalady
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Colorectal Surgery, Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA
- Cancer Biology Department, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA
| | - Joseph Willis
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106
| | - Jason H. Moore
- Norris Cotton Cancer Center, Institute for Quantitative Biomedical Sciences, Department of Genetics, Dartmouth Medical School, Lebanon, NH 03756, USA
| | - Paul J. Tesar
- Department of Genetics, Case Western Reserve University, Cleveland, OH 44106
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Thomas Laframboise
- Department of Genetics, Case Western Reserve University, Cleveland, OH 44106
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Sanford Markowitz
- Department of Genetics, Case Western Reserve University, Cleveland, OH 44106
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Medicine, Case Western Reserve University, Cleveland, OH 44106
| | - Mathieu Lupien
- Norris Cotton Cancer Center, Institute for Quantitative Biomedical Sciences, Department of Genetics, Dartmouth Medical School, Lebanon, NH 03756, USA
| | - Peter C. Scacheri
- Department of Genetics, Case Western Reserve University, Cleveland, OH 44106
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
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Tian C, Yu H, Yang B, Han F, Zheng Y, Bartels CF, Schelling D, Arnold JE, Scacheri PC, Zheng QY. Otitis media in a new mouse model for CHARGE syndrome with a deletion in the Chd7 gene. PLoS One 2012; 7:e34944. [PMID: 22539951 PMCID: PMC3335168 DOI: 10.1371/journal.pone.0034944] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 03/11/2012] [Indexed: 11/17/2022] Open
Abstract
Otitis media is a middle ear disease common in children under three years old. Otitis media can occur in normal individuals with no other symptoms or syndromes, but it is often seen in individuals clinically diagnosed with genetic diseases such as CHARGE syndrome, a complex genetic disease caused by mutation in the Chd7 gene and characterized by multiple birth defects. Although otitis media is common in human CHARGE syndrome patients, it has not been reported in mouse models of CHARGE syndrome. In this study, we report a mouse model with a spontaneous deletion mutation in the Chd7 gene and with chronic otitis media of early onset age accompanied by hearing loss. These mice also exhibit morphological alteration in the Eustachian tubes, dysregulation of epithelial proliferation, and decreased density of middle ear cilia. Gene expression profiling revealed up-regulation of Muc5ac, Muc5b and Tgf-β1 transcripts, the products of which are involved in mucin production and TGF pathway regulation. This is the first mouse model of CHARGE syndrome reported to show otitis media with effusion and it will be valuable for studying the etiology of otitis media and other symptoms in CHARGE syndrome.
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Affiliation(s)
- Cong Tian
- Department of Otolaryngology-Head and Neck Surgery, University Hospitals of Cleveland, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
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21
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Korvala J, Jüppner H, Mäkitie O, Sochett E, Schnabel D, Mora S, Bartels CF, Warman ML, Deraska D, Cole WG, Hartikka H, Ala-Kokko L, Männikkö M. Mutations in LRP5 cause primary osteoporosis without features of OI by reducing Wnt signaling activity. BMC Med Genet 2012; 13:26. [PMID: 22487062 PMCID: PMC3374890 DOI: 10.1186/1471-2350-13-26] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 04/10/2012] [Indexed: 11/23/2022]
Abstract
Background Primary osteoporosis is a rare childhood-onset skeletal condition whose pathogenesis has been largely unknown. We have previously shown that primary osteoporosis can be caused by heterozygous missense mutations in the Low-density lipoprotein receptor-related protein 5 (LRP5) gene, and the role of LRP5 is further investigated here. Methods LRP5 was analyzed in 18 otherwise healthy children and adolescents who had evidence of osteoporosis (manifested as reduced bone mineral density i.e. BMD, recurrent peripheral fractures and/or vertebral compression fractures) but who lacked the clinical features of osteogenesis imperfecta (OI) or other known syndromes linked to low BMD. Also 51 controls were analyzed. Methods used in the genetic analyses included direct sequencing and multiplex ligation-dependent probe amplification (MLPA). In vitro studies were performed using luciferase assay and quantitative real-time polymerase chain reaction (qPCR) to examine the effect of two novel and three previously identified mutations on the activity of canonical Wnt signaling and on expression of tryptophan hydroxylase 1 (Tph1) and 5-hydroxytryptamine (5-Htr1b). Results Two novel LRP5 mutations (c.3446 T > A; p.L1149Q and c.3553 G > A; p.G1185R) were identified in two patients and their affected family members. In vitro analyses showed that one of these novel mutations together with two previously reported mutations (p.C913fs, p.R1036Q) significantly reduced the activity of the canonical Wnt signaling pathway. Such reductions may lead to decreased bone formation, and could explain the bone phenotype. Gut-derived Lrp5 has been shown to regulate serotonin synthesis by controlling the production of serotonin rate-limiting enzyme, Tph1. LRP5 mutations did not affect Tph1 expression, and only one mutant (p.L1149Q) reduced expression of serotonin receptor 5-Htr1b (p < 0.002). Conclusions Our results provide additional information on the role of LRP5 mutations and their effects on the development of juvenile-onset primary osteoporosis, and hence the pathogenesis of the disorder. The mutations causing primary osteoporosis reduce the signaling activity of the canonical Wnt signaling pathway and may therefore result in decreased bone formation. The specific mechanism affecting signaling activity remains to be resolved in future studies.
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Affiliation(s)
- Johanna Korvala
- Oulu Center for Cell-Matrix Research, Biocenter and Department of Medical Biochemistry and Molecular Biology, University of Oulu, Oulu, Finland
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22
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Bartels CF, Scacheri C, White L, Scacheri PC, Bale S. Mutations in the CHD7 gene: the experience of a commercial laboratory. Genet Test Mol Biomarkers 2011; 14:881-91. [PMID: 21158681 DOI: 10.1089/gtmb.2010.0101] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
CHARGE syndrome is an autosomal dominant multisystem disorder caused by mutation in the CHD7 gene, encoding chromodomain helicase DNA-binding protein 7. Molecular diagnostic testing for CHD7 mutation has been available in a clinical setting since 2005. We report here the results from the first 642 unrelated proband samples submitted for testing. Thirty-two percent (n = 203) of patient samples had a heterozygous pathogenic variant identified. The lower mutation rate than that published for well-characterized clinical samples is likely due to referral bias, as samples submitted for clinical testing may be for "rule-out" diagnoses, rather than solely to confirm clinical suspicion. We identified 159 unique pathogenic mutations, and of these, 134 mutations were each seen in a single individual and 25 mutations were found in two to five individuals (n =69). Of the 203 mutations, only 9 were missense, with 107 nonsense, 69 frameshift, and 15 splice-site mutations likely leading to haploinsufficiency at the cellular level. An additional 72 variations identified in the 642 tested samples (11%) were considered to have unknown clinical significance. Copy number changes (deletion/duplication of the entire gene or one/several exons) were found to account for a very small number of cases (n = 3). This cohort represents the largest CHARGE syndrome sample size to date and is intended to serve as a resource for clinicians, genetic counselors, researchers, and other diagnostic laboratories.
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Affiliation(s)
- Cynthia F Bartels
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio 44016, USA
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23
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Abstract
The six mammalian CCN genes (Cyr61, CTGF, Nov, WISP1, WISP2, WISP3) encode a family of secreted, cysteine-rich, multimodular proteins having roles in cell proliferation, adhesion, migration, and differentiation during embryogenesis, wound healing, and angiogenesis. We used bioinformatics to identify 9 CCN genes in zebrafish (zCCNs), 6 of which have not been previously described. When compared with mammalian CCN family members, 3 were paralogs of Cyr61, 2 of CTGF, 2 of WISP1, 1 of WISP2, and 1 of WISP3. No paralog of Nov was found. In situ hybridization was performed to characterize the sites of expression of the zCCNs during early zebrafish development. zCCNs demonstrated both unique and overlapping patterns of expression, suggesting potential division of labor between orthologous genes and providing an alternate approach to gene function studies that will complement studies in mammalian models. Developmental Dynamics 239:1755–1767, 2010. © 2010 Wiley-Liss, Inc.
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Affiliation(s)
- Carol A Fernando
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio, USA
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24
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Schnetz MP, Handoko L, Akhtar-Zaidi B, Bartels CF, Pereira CF, Fisher AG, Adams DJ, Flicek P, Crawford GE, LaFramboise T, Tesar P, Wei CL, Scacheri PC. CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression. PLoS Genet 2010; 6:e1001023. [PMID: 20657823 PMCID: PMC2904778 DOI: 10.1371/journal.pgen.1001023] [Citation(s) in RCA: 183] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 06/14/2010] [Indexed: 01/22/2023] Open
Abstract
CHD7 is one of nine members of the chromodomain helicase DNA–binding domain family of ATP–dependent chromatin remodeling enzymes found in mammalian cells. De novo mutation of CHD7 is a major cause of CHARGE syndrome, a genetic condition characterized by multiple congenital anomalies. To gain insights to the function of CHD7, we used the technique of chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP–Seq) to map CHD7 sites in mouse ES cells. We identified 10,483 sites on chromatin bound by CHD7 at high confidence. Most of the CHD7 sites show features of gene enhancer elements. Specifically, CHD7 sites are predominantly located distal to transcription start sites, contain high levels of H3K4 mono-methylation, found within open chromatin that is hypersensitive to DNase I digestion, and correlate with ES cell-specific gene expression. Moreover, CHD7 co-localizes with P300, a known enhancer-binding protein and strong predictor of enhancer activity. Correlations with 18 other factors mapped by ChIP–seq in mouse ES cells indicate that CHD7 also co-localizes with ES cell master regulators OCT4, SOX2, and NANOG. Correlations between CHD7 sites and global gene expression profiles obtained from Chd7+/+, Chd7+/−, and Chd7−/− ES cells indicate that CHD7 functions at enhancers as a transcriptional rheostat to modulate, or fine-tune the expression levels of ES–specific genes. CHD7 can modulate genes in either the positive or negative direction, although negative regulation appears to be the more direct effect of CHD7 binding. These data indicate that enhancer-binding proteins can limit gene expression and are not necessarily co-activators. Although ES cells are not likely to be affected in CHARGE syndrome, we propose that enhancer-mediated gene dysregulation contributes to disease pathogenesis and that the critical CHD7 target genes may be subject to positive or negative regulation. The gene encoding chromodomain helicase DNA–binding protein 7 (CHD7) is required for normal mammalian development. In humans, genetic mutations in CHD7 lead to CHARGE syndrome, a disorder characterized by multiple birth defects. In previous studies, CHD7 was shown to localize to the cell nucleus and bind to specific sites on chromatin. However, the genome-wide distribution of CHD7 on chromatin and its function are not known. Here, we identified 10,483 sites on chromatin bound by CHD7 in mouse embryonic stem cells. Many of these sites are gene enhancer elements suspected to be involved in turning on genes. We show CHD7 functions at these loci to fine-tune the levels of genes that are specifically expressed in mouse ES cells. This modulation is mediated through several proteins that bind together with CHD7 at enhancer elements and can occur in either direction. These findings suggest CHARGE syndrome is the result of key genes that are improperly expressed during development. These key genes are currently unknown but are likely to be tissue-specific and may be upregulated or downregulated in response to CHD7 mutation.
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Affiliation(s)
- Michael P. Schnetz
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Lusy Handoko
- Genome Technology and Biology Group, Genome Institute of Singapore, Singapore, Singapore
| | - Batool Akhtar-Zaidi
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Cynthia F. Bartels
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - C. Filipe Pereira
- Lymphocyte Development Group, Medical Research Council Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital, London, United Kingdom
| | - Amanda G. Fisher
- Lymphocyte Development Group, Medical Research Council Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital, London, United Kingdom
| | - David J. Adams
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Paul Flicek
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Gregory E. Crawford
- Institute for Genome Sciences & Policy and Department of Pediatrics, Duke University, Durham, North Carolina, United States of America
| | - Thomas LaFramboise
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Paul Tesar
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Chia-Lin Wei
- Genome Technology and Biology Group, Genome Institute of Singapore, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Peter C. Scacheri
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail:
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25
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Schnetz MP, Bartels CF, Shastri K, Balasubramanian D, Zentner GE, Balaji R, Zhang X, Song L, Wang Z, Laframboise T, Crawford GE, Scacheri PC. Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns. Genome Res 2009; 19:590-601. [PMID: 19251738 DOI: 10.1101/gr.086983.108] [Citation(s) in RCA: 194] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
CHD7 is a member of the chromodomain helicase DNA binding domain family of ATP-dependent chromatin remodeling enzymes. De novo mutation of the CHD7 gene is a major cause of CHARGE syndrome, a genetic disease characterized by a complex constellation of birth defects (Coloboma of the eye, Heart defects, Atresia of the choanae, severe Retardation of growth and development, Genital abnormalities, and Ear abnormalities). To gain insight into the function of CHD7, we mapped the distribution of the CHD7 protein on chromatin using the approach of chromatin immunoprecipitation on tiled microarrays (ChIP-chip). These studies were performed in human colorectal carcinoma cells, human neuroblastoma cells, and mouse embryonic stem (ES) cells before and after differentiation into neural precursor cells. The results indicate that CHD7 localizes to discrete locations along chromatin that are specific to each cell type, and that the cell-specific binding of CHD7 correlates with a subset of histone H3 methylated at lysine 4 (H3K4me). The CHD7 sites change concomitantly with H3K4me patterns during ES cell differentiation, suggesting that H3K4me is part of the epigenetic signature that defines lineage-specific association of CHD7 with specific sites on chromatin. Furthermore, the CHD7 sites are predominantly located distal to transcription start sites, most often contained within DNase hypersensitive sites, frequently conserved, and near genes expressed at relatively high levels. These features are similar to those of gene enhancer elements, raising the possibility that CHD7 functions in enhancer mediated transcription, and that the congenital anomalies in CHARGE syndrome are due to alterations in transcription of tissue-specific genes normally regulated by CHD7 during development.
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Affiliation(s)
- Michael P Schnetz
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio 44106, USA
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26
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Zhang X, Guo C, Chen Y, Shulha HP, Schnetz MP, LaFramboise T, Bartels CF, Markowitz S, Weng Z, Scacheri PC, Wang Z. Epitope tagging of endogenous proteins for genome-wide ChIP-chip studies. Nat Methods 2008; 5:163-5. [PMID: 18176569 DOI: 10.1038/nmeth1170] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2007] [Accepted: 11/26/2007] [Indexed: 01/30/2023]
Abstract
We developed a strategy to introduce epitope tag-encoding DNA into endogenous loci by homologous recombination-mediated 'knock-in'. The tagging method is straightforward, can be applied to many loci and several human somatic cell lines, and can facilitate many functional analyses including western blot, immunoprecipitation, immunofluorescence and chromatin immunoprecipitation-microarray (ChIP-chip). The knock-in approach provides a general solution for the study of proteins to which antibodies are substandard or not available.
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Affiliation(s)
- Xiaodong Zhang
- Department of Genetics and Case Comprehensive Cancer Center, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
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27
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Olney RC, Bükülmez H, Bartels CF, Prickett TCR, Espiner EA, Potter LR, Warman ML. Heterozygous mutations in natriuretic peptide receptor-B (NPR2) are associated with short stature. J Clin Endocrinol Metab 2006; 91:1229-32. [PMID: 16384845 DOI: 10.1210/jc.2005-1949] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT C-type natriuretic peptide (CNP) is an important regulator of skeletal growth. Loss-of-function mutations affecting the CNP receptor natriuretic peptide receptor-B (gene NPR2) cause the autosomal recessive skeletal dysplasia, acromesomelic dysplasia, Maroteaux type (AMDM). The phenotype of heterozygous carriers of NPR2 mutations is less clear. OBJECTIVE The objective of the study was to determine the phenotypic features of heterozygous carriers of NPR2 mutations. DESIGN AND SETTING This was a case-control study from the general community. SUBJECTS Thirty-nine members of a family in which one member has AMDM were studied. INTERVENTION This was an observational study. MAIN OUTCOME MEASURE The primary measure was stature, with the hypothesis that carriers have reduced stature compared with noncarriers. RESULTS Sixteen family members were NPR2 mutation carriers. Height z-scores of these carriers were -1.8 +/- 1.1 (mean +/- sd), which was significantly less than the 23 noncarrier family members (-0.4 +/- 0.8, P < 0.0005) and the general population (P < 0.0005). However, there was no difference in body proportion between carriers and noncarriers. The proband with AMDM had low IGF-I levels and evidence of GH resistance, as well as very high plasma levels of CNP and its amino-terminal propeptide. Levels of these peptides were normal in the heterozygous carriers. CONCLUSIONS We have shown that heterozygous mutations in NPR2 are associated with short stature. Assuming one in 700 people unknowingly carry an NPR2 mutation, our data suggest that approximately one in 30 individuals with idiopathic short stature are carriers of NPR2 mutations.
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Affiliation(s)
- Robert C Olney
- Division of Endocrinology, Nemours Children's Clinic, Jacksonville, FL 32207, USA.
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28
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Ai M, Heeger S, Bartels CF, Schelling DK. Clinical and molecular findings in osteoporosis-pseudoglioma syndrome. Am J Hum Genet 2005; 77:741-53. [PMID: 16252235 PMCID: PMC1271384 DOI: 10.1086/497706] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.1] [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: 06/20/2005] [Accepted: 08/10/2005] [Indexed: 01/17/2023] Open
Abstract
Mutations in the low-density lipoprotein receptor-related protein 5 gene (LRP5) cause autosomal recessive osteoporosis-pseudoglioma syndrome (OPPG). We sequenced the coding exons of LRP5 in 37 probands suspected of having OPPG on the basis of the co-occurrence of severe congenital or childhood-onset visual impairment with bone fragility or osteoporosis recognized by young adulthood. We found two putative mutant alleles in 26 probands, only one mutant allele in 4 probands, and no mutant alleles in 7 probands. Looking for digenic inheritance, we sequenced the genes encoding the functionally related receptor LRP6, an LRP5 coreceptor FZD4, and an LRP5 ligand, NDP, in the four probands with one mutant allele, and, looking for locus heterogeneity, we sequenced FZD4 and NDP in the seven probands with no mutations, but we found no additional mutations. When we compared clinical features between probands with and without LRP5 mutations, we found no difference in the severity of skeletal disease, prevalence of cognitive impairment, or family history of consanguinity. However, four of the seven probands without detectable mutations had eye pathology that differed from pathology previously described for OPPG. Since many LRP5 mutations are missense changes, to differentiate between a disease-causing mutation and a benign variant, we measured the ability of wild-type and mutant LRP5 to transduce Wnt and Norrin signal ex vivo. Each of the seven OPPG mutations tested, had reduced signal transduction compared with wild-type mutations. These results indicate that early bilateral vitreoretinal eye pathology coupled with skeletal fragility is a strong predictor of LRP5 mutation and that mutations in LRP5 cause OPPG by impairing Wnt and Norrin signal transduction.
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Affiliation(s)
- Minrong Ai
- Department of Genetics and Center for Human Genetics, Case School of Medicine and University Hospitals of Cleveland, Cleveland, OH, 44106, USA
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Rhee DK, Marcelino J, Al-Mayouf S, Schelling DK, Bartels CF, Cui Y, Laxer R, Goldbach-Mansky R, Warman ML. Consequences of Disease-causing Mutations on Lubricin Protein Synthesis, Secretion, and Post-translational Processing. J Biol Chem 2005; 280:31325-32. [PMID: 16000300 DOI: 10.1074/jbc.m505401200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Lubricin, a protein product of the gene PRG4, is a secreted mucin-like proteoglycan that is a major lubricant in articulating joints. Mutations in PRG4 cause the autosomal recessive, human disorder camptodactyly-arthropathy-coxa vara-pericarditis syndrome. We developed rabbit polyclonal antibodies against human lubricin to determine the consequence of disease-causing mutations at the protein level and to study the protein's normal post-translational processing. Antiserum generated against an epitope in the amino-terminal portion of lubricin detected protein in wild-type synovial fluid and in conditioned media from wild-type cultured synoviocytes. However, the antiserum did not detect lubricin in synovial fluid or cultured synoviocytes from several patients with frameshift or nonsense mutations in PRG4. Antiserum generated against an epitope in the protein's carboxyl-terminal, hemopexin-like domain identified a post-translational cleavage event in wild-type lubricin, mediated by a subtilisin-like proprotein convertase (SPC). Interestingly, in contrast to wild-type lubricin, one disease-causing mutation that removes the last 8 amino acids of the protein, including a conserved cysteine residue, was not cleaved within the hemopexin-like domain when expressed in COS-7 cells. This suggests that formation of an intrachain disulfide bond is required for SPC-mediated cleavage and that SPC-mediated cleavage is essential to protein function.
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Affiliation(s)
- David K Rhee
- Department of Genetics and Center for Human Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 44106, USA
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Schopfer LM, Voelker T, Bartels CF, Thompson CM, Lockridge O. Reaction kinetics of biotinylated organophosphorus toxicant, FP-biotin, with human acetylcholinesterase and human butyrylcholinesterase. Chem Res Toxicol 2005; 18:747-54. [PMID: 15833035 DOI: 10.1021/tx049672j] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A biotinylated organophosphate could be useful for identifying proteins that react with organophosphorus toxicants (OP). FP-biotin, 10-(fluoroethoxyphosphinyl)-N-(biotinamidopentyl)decanamide, was synthesized and found to be stable in methanol and chloroform but less stable in water. Because acetylcholinesterase (AChE, EC 3.1.1.7) and butyrylcholinesterase (BChE, EC 3.1.1.8) are known to be sensitive targets of OP, their reactivity with FP-biotin was tested. The rate constant for reaction with human AChE was 1.8 x 10(7) M(-1) min(-1), and for human BChE, it was 1.6 x 10(8) M(-1) min(-1). A phosphorus stereoisomer, constituting about 50% of the FP-biotin preparation, appeared to be the reactive species. The binding affinity was estimated to be >85 nM for AChE and >5.8 nM for BChE. It was concluded that FP-biotin is a potent OP, well-suited for searching for new biomarkers of OP exposure.
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Affiliation(s)
- Lawrence M Schopfer
- Eppley Institute, University of Nebraska Medical Center, Omaha, Nebraska 68198-6805, USA.
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Bartels CF, Bükülmez H, Padayatti P, Rhee DK, van Ravenswaaij-Arts C, Pauli RM, Mundlos S, Chitayat D, Shih LY, Al-Gazali LI, Kant S, Cole T, Morton J, Cormier-Daire V, Faivre L, Lees M, Kirk J, Mortier GR, Leroy J, Zabel B, Kim CA, Crow Y, Braverman NE, van den Akker F, Warman ML. Mutations in the transmembrane natriuretic peptide receptor NPR-B impair skeletal growth and cause acromesomelic dysplasia, type Maroteaux. Am J Hum Genet 2004; 75:27-34. [PMID: 15146390 PMCID: PMC1182004 DOI: 10.1086/422013] [Citation(s) in RCA: 232] [Impact Index Per Article: 11.6] [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: 01/13/2004] [Accepted: 04/09/2004] [Indexed: 11/03/2022] Open
Abstract
The homodimeric transmembrane receptor natriuretic peptide receptor B (NPR-B [also known as guanylate cyclase B, GC-B, and GUC2B]; gene name NPR2) produces cytoplasmic cyclic GMP from GTP on binding its extracellular ligand, C-type natriuretic peptide (CNP). CNP has previously been implicated in the regulation of skeletal growth in transgenic and knockout mice. The autosomal recessive skeletal dysplasia known as "acromesomelic dysplasia, type Maroteaux" (AMDM) maps to an interval that contains NPR2. We sequenced DNA from 21 families affected by AMDM and found 4 nonsense mutations, 4 frameshift mutations, 2 splice-site mutations, and 11 missense mutations. Molecular modeling was used to examine the putative protein change brought about by each missense mutation. Three missense mutations were tested in a functional assay and were found to have markedly deficient guanylyl cyclase activity. We also found that obligate carriers of NPR2 mutations have heights that are below the mean for matched controls. We conclude that, although NPR-B is expressed in a number of tissues, its major role is in the regulation of skeletal growth.
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Affiliation(s)
- Cynthia F. Bartels
- Departments of Genetics, Epidemiology and Biostatistics, Biochemistry, and Pediatrics, Case Western Reserve University School of Medicine, Center for Human Genetics, University Hospitals of Cleveland, and Department of Pediatrics, Metro Health Medical Center, Cleveland; Department of Human Genetics, University Medical Centre Nijmegen, Nijmegen, The Netherlands; Departments of Pediatrics and Medical Genetics, University of Wisconsin–Madison, Madison, WI; Institut für Medizinische Genetik Charité, Campus Virchow, Berlin; Medical Genetics, Hospital for Sick Children, Toronto; Center for Human and Molecular Genetics, University of Medicine and Dentistry of New Jersey, Newark, NJ; Department of Pediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates; Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands; Clinical Genetics Unit, Birmingham Women’s Healthcare, and Department of Pediatric Endocrinology, Birmingham Children’s Hospital, Birmingham, United Kingdom; Department of Medical Genetics, Hopital Necker, Paris; Genetics Center, Hopital d’Enfants, Dijon, France; Department of Clinical Genetics, Great Ormond Street Hospital, London; Department of Medical Genetics, Ghent University Hospital, Ghent, Belgium; Children’s Hospital, University of Mainz, Mainz, Germany; Department of Genetics, University of São Paulo, São Paulo, Brazil; Department of Clinical Genetics, The Leeds Teaching Hospital, Leeds, United Kingdom; and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore
| | - Hülya Bükülmez
- Departments of Genetics, Epidemiology and Biostatistics, Biochemistry, and Pediatrics, Case Western Reserve University School of Medicine, Center for Human Genetics, University Hospitals of Cleveland, and Department of Pediatrics, Metro Health Medical Center, Cleveland; Department of Human Genetics, University Medical Centre Nijmegen, Nijmegen, The Netherlands; Departments of Pediatrics and Medical Genetics, University of Wisconsin–Madison, Madison, WI; Institut für Medizinische Genetik Charité, Campus Virchow, Berlin; Medical Genetics, Hospital for Sick Children, Toronto; Center for Human and Molecular Genetics, University of Medicine and Dentistry of New Jersey, Newark, NJ; Department of Pediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates; Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands; Clinical Genetics Unit, Birmingham Women’s Healthcare, and Department of Pediatric Endocrinology, Birmingham Children’s Hospital, Birmingham, United Kingdom; Department of Medical Genetics, Hopital Necker, Paris; Genetics Center, Hopital d’Enfants, Dijon, France; Department of Clinical Genetics, Great Ormond Street Hospital, London; Department of Medical Genetics, Ghent University Hospital, Ghent, Belgium; Children’s Hospital, University of Mainz, Mainz, Germany; Department of Genetics, University of São Paulo, São Paulo, Brazil; Department of Clinical Genetics, The Leeds Teaching Hospital, Leeds, United Kingdom; and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore
| | - Pius Padayatti
- Departments of Genetics, Epidemiology and Biostatistics, Biochemistry, and Pediatrics, Case Western Reserve University School of Medicine, Center for Human Genetics, University Hospitals of Cleveland, and Department of Pediatrics, Metro Health Medical Center, Cleveland; Department of Human Genetics, University Medical Centre Nijmegen, Nijmegen, The Netherlands; Departments of Pediatrics and Medical Genetics, University of Wisconsin–Madison, Madison, WI; Institut für Medizinische Genetik Charité, Campus Virchow, Berlin; Medical Genetics, Hospital for Sick Children, Toronto; Center for Human and Molecular Genetics, University of Medicine and Dentistry of New Jersey, Newark, NJ; Department of Pediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates; Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands; Clinical Genetics Unit, Birmingham Women’s Healthcare, and Department of Pediatric Endocrinology, Birmingham Children’s Hospital, Birmingham, United Kingdom; Department of Medical Genetics, Hopital Necker, Paris; Genetics Center, Hopital d’Enfants, Dijon, France; Department of Clinical Genetics, Great Ormond Street Hospital, London; Department of Medical Genetics, Ghent University Hospital, Ghent, Belgium; Children’s Hospital, University of Mainz, Mainz, Germany; Department of Genetics, University of São Paulo, São Paulo, Brazil; Department of Clinical Genetics, The Leeds Teaching Hospital, Leeds, United Kingdom; and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore
| | - David K. Rhee
- Departments of Genetics, Epidemiology and Biostatistics, Biochemistry, and Pediatrics, Case Western Reserve University School of Medicine, Center for Human Genetics, University Hospitals of Cleveland, and Department of Pediatrics, Metro Health Medical Center, Cleveland; Department of Human Genetics, University Medical Centre Nijmegen, Nijmegen, The Netherlands; Departments of Pediatrics and Medical Genetics, University of Wisconsin–Madison, Madison, WI; Institut für Medizinische Genetik Charité, Campus Virchow, Berlin; Medical Genetics, Hospital for Sick Children, Toronto; Center for Human and Molecular Genetics, University of Medicine and Dentistry of New Jersey, Newark, NJ; Department of Pediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates; Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands; Clinical Genetics Unit, Birmingham Women’s Healthcare, and Department of Pediatric Endocrinology, Birmingham Children’s Hospital, Birmingham, United Kingdom; Department of Medical Genetics, Hopital Necker, Paris; Genetics Center, Hopital d’Enfants, Dijon, France; Department of Clinical Genetics, Great Ormond Street Hospital, London; Department of Medical Genetics, Ghent University Hospital, Ghent, Belgium; Children’s Hospital, University of Mainz, Mainz, Germany; Department of Genetics, University of São Paulo, São Paulo, Brazil; Department of Clinical Genetics, The Leeds Teaching Hospital, Leeds, United Kingdom; and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore
| | - Conny van Ravenswaaij-Arts
- Departments of Genetics, Epidemiology and Biostatistics, Biochemistry, and Pediatrics, Case Western Reserve University School of Medicine, Center for Human Genetics, University Hospitals of Cleveland, and Department of Pediatrics, Metro Health Medical Center, Cleveland; Department of Human Genetics, University Medical Centre Nijmegen, Nijmegen, The Netherlands; Departments of Pediatrics and Medical Genetics, University of Wisconsin–Madison, Madison, WI; Institut für Medizinische Genetik Charité, Campus Virchow, Berlin; Medical Genetics, Hospital for Sick Children, Toronto; Center for Human and Molecular Genetics, University of Medicine and Dentistry of New Jersey, Newark, NJ; Department of Pediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates; Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands; Clinical Genetics Unit, Birmingham Women’s Healthcare, and Department of Pediatric Endocrinology, Birmingham Children’s Hospital, Birmingham, United Kingdom; Department of Medical Genetics, Hopital Necker, Paris; Genetics Center, Hopital d’Enfants, Dijon, France; Department of Clinical Genetics, Great Ormond Street Hospital, London; Department of Medical Genetics, Ghent University Hospital, Ghent, Belgium; Children’s Hospital, University of Mainz, Mainz, Germany; Department of Genetics, University of São Paulo, São Paulo, Brazil; Department of Clinical Genetics, The Leeds Teaching Hospital, Leeds, United Kingdom; and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore
| | - Richard M. Pauli
- Departments of Genetics, Epidemiology and Biostatistics, Biochemistry, and Pediatrics, Case Western Reserve University School of Medicine, Center for Human Genetics, University Hospitals of Cleveland, and Department of Pediatrics, Metro Health Medical Center, Cleveland; Department of Human Genetics, University Medical Centre Nijmegen, Nijmegen, The Netherlands; Departments of Pediatrics and Medical Genetics, University of Wisconsin–Madison, Madison, WI; Institut für Medizinische Genetik Charité, Campus Virchow, Berlin; Medical Genetics, Hospital for Sick Children, Toronto; Center for Human and Molecular Genetics, University of Medicine and Dentistry of New Jersey, Newark, NJ; Department of Pediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates; Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands; Clinical Genetics Unit, Birmingham Women’s Healthcare, and Department of Pediatric Endocrinology, Birmingham Children’s Hospital, Birmingham, United Kingdom; Department of Medical Genetics, Hopital Necker, Paris; Genetics Center, Hopital d’Enfants, Dijon, France; Department of Clinical Genetics, Great Ormond Street Hospital, London; Department of Medical Genetics, Ghent University Hospital, Ghent, Belgium; Children’s Hospital, University of Mainz, Mainz, Germany; Department of Genetics, University of São Paulo, São Paulo, Brazil; Department of Clinical Genetics, The Leeds Teaching Hospital, Leeds, United Kingdom; and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore
| | - Stefan Mundlos
- Departments of Genetics, Epidemiology and Biostatistics, Biochemistry, and Pediatrics, Case Western Reserve University School of Medicine, Center for Human Genetics, University Hospitals of Cleveland, and Department of Pediatrics, Metro Health Medical Center, Cleveland; Department of Human Genetics, University Medical Centre Nijmegen, Nijmegen, The Netherlands; Departments of Pediatrics and Medical Genetics, University of Wisconsin–Madison, Madison, WI; Institut für Medizinische Genetik Charité, Campus Virchow, Berlin; Medical Genetics, Hospital for Sick Children, Toronto; Center for Human and Molecular Genetics, University of Medicine and Dentistry of New Jersey, Newark, NJ; Department of Pediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates; Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands; Clinical Genetics Unit, Birmingham Women’s Healthcare, and Department of Pediatric Endocrinology, Birmingham Children’s Hospital, Birmingham, United Kingdom; Department of Medical Genetics, Hopital Necker, Paris; Genetics Center, Hopital d’Enfants, Dijon, France; Department of Clinical Genetics, Great Ormond Street Hospital, London; Department of Medical Genetics, Ghent University Hospital, Ghent, Belgium; Children’s Hospital, University of Mainz, Mainz, Germany; Department of Genetics, University of São Paulo, São Paulo, Brazil; Department of Clinical Genetics, The Leeds Teaching Hospital, Leeds, United Kingdom; and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore
| | - David Chitayat
- Departments of Genetics, Epidemiology and Biostatistics, Biochemistry, and Pediatrics, Case Western Reserve University School of Medicine, Center for Human Genetics, University Hospitals of Cleveland, and Department of Pediatrics, Metro Health Medical Center, Cleveland; Department of Human Genetics, University Medical Centre Nijmegen, Nijmegen, The Netherlands; Departments of Pediatrics and Medical Genetics, University of Wisconsin–Madison, Madison, WI; Institut für Medizinische Genetik Charité, Campus Virchow, Berlin; Medical Genetics, Hospital for Sick Children, Toronto; Center for Human and Molecular Genetics, University of Medicine and Dentistry of New Jersey, Newark, NJ; Department of Pediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates; Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands; Clinical Genetics Unit, Birmingham Women’s Healthcare, and Department of Pediatric Endocrinology, Birmingham Children’s Hospital, Birmingham, United Kingdom; Department of Medical Genetics, Hopital Necker, Paris; Genetics Center, Hopital d’Enfants, Dijon, France; Department of Clinical Genetics, Great Ormond Street Hospital, London; Department of Medical Genetics, Ghent University Hospital, Ghent, Belgium; Children’s Hospital, University of Mainz, Mainz, Germany; Department of Genetics, University of São Paulo, São Paulo, Brazil; Department of Clinical Genetics, The Leeds Teaching Hospital, Leeds, United Kingdom; and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore
| | - Ling-Yu Shih
- Departments of Genetics, Epidemiology and Biostatistics, Biochemistry, and Pediatrics, Case Western Reserve University School of Medicine, Center for Human Genetics, University Hospitals of Cleveland, and Department of Pediatrics, Metro Health Medical Center, Cleveland; Department of Human Genetics, University Medical Centre Nijmegen, Nijmegen, The Netherlands; Departments of Pediatrics and Medical Genetics, University of Wisconsin–Madison, Madison, WI; Institut für Medizinische Genetik Charité, Campus Virchow, Berlin; Medical Genetics, Hospital for Sick Children, Toronto; Center for Human and Molecular Genetics, University of Medicine and Dentistry of New Jersey, Newark, NJ; Department of Pediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates; Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands; Clinical Genetics Unit, Birmingham Women’s Healthcare, and Department of Pediatric Endocrinology, Birmingham Children’s Hospital, Birmingham, United Kingdom; Department of Medical Genetics, Hopital Necker, Paris; Genetics Center, Hopital d’Enfants, Dijon, France; Department of Clinical Genetics, Great Ormond Street Hospital, London; Department of Medical Genetics, Ghent University Hospital, Ghent, Belgium; Children’s Hospital, University of Mainz, Mainz, Germany; Department of Genetics, University of São Paulo, São Paulo, Brazil; Department of Clinical Genetics, The Leeds Teaching Hospital, Leeds, United Kingdom; and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore
| | - Lihadh I. Al-Gazali
- Departments of Genetics, Epidemiology and Biostatistics, Biochemistry, and Pediatrics, Case Western Reserve University School of Medicine, Center for Human Genetics, University Hospitals of Cleveland, and Department of Pediatrics, Metro Health Medical Center, Cleveland; Department of Human Genetics, University Medical Centre Nijmegen, Nijmegen, The Netherlands; Departments of Pediatrics and Medical Genetics, University of Wisconsin–Madison, Madison, WI; Institut für Medizinische Genetik Charité, Campus Virchow, Berlin; Medical Genetics, Hospital for Sick Children, Toronto; Center for Human and Molecular Genetics, University of Medicine and Dentistry of New Jersey, Newark, NJ; Department of Pediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates; Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands; Clinical Genetics Unit, Birmingham Women’s Healthcare, and Department of Pediatric Endocrinology, Birmingham Children’s Hospital, Birmingham, United Kingdom; Department of Medical Genetics, Hopital Necker, Paris; Genetics Center, Hopital d’Enfants, Dijon, France; Department of Clinical Genetics, Great Ormond Street Hospital, London; Department of Medical Genetics, Ghent University Hospital, Ghent, Belgium; Children’s Hospital, University of Mainz, Mainz, Germany; Department of Genetics, University of São Paulo, São Paulo, Brazil; Department of Clinical Genetics, The Leeds Teaching Hospital, Leeds, United Kingdom; and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore
| | - Sarina Kant
- Departments of Genetics, Epidemiology and Biostatistics, Biochemistry, and Pediatrics, Case Western Reserve University School of Medicine, Center for Human Genetics, University Hospitals of Cleveland, and Department of Pediatrics, Metro Health Medical Center, Cleveland; Department of Human Genetics, University Medical Centre Nijmegen, Nijmegen, The Netherlands; Departments of Pediatrics and Medical Genetics, University of Wisconsin–Madison, Madison, WI; Institut für Medizinische Genetik Charité, Campus Virchow, Berlin; Medical Genetics, Hospital for Sick Children, Toronto; Center for Human and Molecular Genetics, University of Medicine and Dentistry of New Jersey, Newark, NJ; Department of Pediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates; Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands; Clinical Genetics Unit, Birmingham Women’s Healthcare, and Department of Pediatric Endocrinology, Birmingham Children’s Hospital, Birmingham, United Kingdom; Department of Medical Genetics, Hopital Necker, Paris; Genetics Center, Hopital d’Enfants, Dijon, France; Department of Clinical Genetics, Great Ormond Street Hospital, London; Department of Medical Genetics, Ghent University Hospital, Ghent, Belgium; Children’s Hospital, University of Mainz, Mainz, Germany; Department of Genetics, University of São Paulo, São Paulo, Brazil; Department of Clinical Genetics, The Leeds Teaching Hospital, Leeds, United Kingdom; and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore
| | - Trevor Cole
- Departments of Genetics, Epidemiology and Biostatistics, Biochemistry, and Pediatrics, Case Western Reserve University School of Medicine, Center for Human Genetics, University Hospitals of Cleveland, and Department of Pediatrics, Metro Health Medical Center, Cleveland; Department of Human Genetics, University Medical Centre Nijmegen, Nijmegen, The Netherlands; Departments of Pediatrics and Medical Genetics, University of Wisconsin–Madison, Madison, WI; Institut für Medizinische Genetik Charité, Campus Virchow, Berlin; Medical Genetics, Hospital for Sick Children, Toronto; Center for Human and Molecular Genetics, University of Medicine and Dentistry of New Jersey, Newark, NJ; Department of Pediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates; Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands; Clinical Genetics Unit, Birmingham Women’s Healthcare, and Department of Pediatric Endocrinology, Birmingham Children’s Hospital, Birmingham, United Kingdom; Department of Medical Genetics, Hopital Necker, Paris; Genetics Center, Hopital d’Enfants, Dijon, France; Department of Clinical Genetics, Great Ormond Street Hospital, London; Department of Medical Genetics, Ghent University Hospital, Ghent, Belgium; Children’s Hospital, University of Mainz, Mainz, Germany; Department of Genetics, University of São Paulo, São Paulo, Brazil; Department of Clinical Genetics, The Leeds Teaching Hospital, Leeds, United Kingdom; and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore
| | - Jenny Morton
- Departments of Genetics, Epidemiology and Biostatistics, Biochemistry, and Pediatrics, Case Western Reserve University School of Medicine, Center for Human Genetics, University Hospitals of Cleveland, and Department of Pediatrics, Metro Health Medical Center, Cleveland; Department of Human Genetics, University Medical Centre Nijmegen, Nijmegen, The Netherlands; Departments of Pediatrics and Medical Genetics, University of Wisconsin–Madison, Madison, WI; Institut für Medizinische Genetik Charité, Campus Virchow, Berlin; Medical Genetics, Hospital for Sick Children, Toronto; Center for Human and Molecular Genetics, University of Medicine and Dentistry of New Jersey, Newark, NJ; Department of Pediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates; Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands; Clinical Genetics Unit, Birmingham Women’s Healthcare, and Department of Pediatric Endocrinology, Birmingham Children’s Hospital, Birmingham, United Kingdom; Department of Medical Genetics, Hopital Necker, Paris; Genetics Center, Hopital d’Enfants, Dijon, France; Department of Clinical Genetics, Great Ormond Street Hospital, London; Department of Medical Genetics, Ghent University Hospital, Ghent, Belgium; Children’s Hospital, University of Mainz, Mainz, Germany; Department of Genetics, University of São Paulo, São Paulo, Brazil; Department of Clinical Genetics, The Leeds Teaching Hospital, Leeds, United Kingdom; and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore
| | - Valérie Cormier-Daire
- Departments of Genetics, Epidemiology and Biostatistics, Biochemistry, and Pediatrics, Case Western Reserve University School of Medicine, Center for Human Genetics, University Hospitals of Cleveland, and Department of Pediatrics, Metro Health Medical Center, Cleveland; Department of Human Genetics, University Medical Centre Nijmegen, Nijmegen, The Netherlands; Departments of Pediatrics and Medical Genetics, University of Wisconsin–Madison, Madison, WI; Institut für Medizinische Genetik Charité, Campus Virchow, Berlin; Medical Genetics, Hospital for Sick Children, Toronto; Center for Human and Molecular Genetics, University of Medicine and Dentistry of New Jersey, Newark, NJ; Department of Pediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates; Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands; Clinical Genetics Unit, Birmingham Women’s Healthcare, and Department of Pediatric Endocrinology, Birmingham Children’s Hospital, Birmingham, United Kingdom; Department of Medical Genetics, Hopital Necker, Paris; Genetics Center, Hopital d’Enfants, Dijon, France; Department of Clinical Genetics, Great Ormond Street Hospital, London; Department of Medical Genetics, Ghent University Hospital, Ghent, Belgium; Children’s Hospital, University of Mainz, Mainz, Germany; Department of Genetics, University of São Paulo, São Paulo, Brazil; Department of Clinical Genetics, The Leeds Teaching Hospital, Leeds, United Kingdom; and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore
| | - Laurence Faivre
- Departments of Genetics, Epidemiology and Biostatistics, Biochemistry, and Pediatrics, Case Western Reserve University School of Medicine, Center for Human Genetics, University Hospitals of Cleveland, and Department of Pediatrics, Metro Health Medical Center, Cleveland; Department of Human Genetics, University Medical Centre Nijmegen, Nijmegen, The Netherlands; Departments of Pediatrics and Medical Genetics, University of Wisconsin–Madison, Madison, WI; Institut für Medizinische Genetik Charité, Campus Virchow, Berlin; Medical Genetics, Hospital for Sick Children, Toronto; Center for Human and Molecular Genetics, University of Medicine and Dentistry of New Jersey, Newark, NJ; Department of Pediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates; Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands; Clinical Genetics Unit, Birmingham Women’s Healthcare, and Department of Pediatric Endocrinology, Birmingham Children’s Hospital, Birmingham, United Kingdom; Department of Medical Genetics, Hopital Necker, Paris; Genetics Center, Hopital d’Enfants, Dijon, France; Department of Clinical Genetics, Great Ormond Street Hospital, London; Department of Medical Genetics, Ghent University Hospital, Ghent, Belgium; Children’s Hospital, University of Mainz, Mainz, Germany; Department of Genetics, University of São Paulo, São Paulo, Brazil; Department of Clinical Genetics, The Leeds Teaching Hospital, Leeds, United Kingdom; and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore
| | - Melissa Lees
- Departments of Genetics, Epidemiology and Biostatistics, Biochemistry, and Pediatrics, Case Western Reserve University School of Medicine, Center for Human Genetics, University Hospitals of Cleveland, and Department of Pediatrics, Metro Health Medical Center, Cleveland; Department of Human Genetics, University Medical Centre Nijmegen, Nijmegen, The Netherlands; Departments of Pediatrics and Medical Genetics, University of Wisconsin–Madison, Madison, WI; Institut für Medizinische Genetik Charité, Campus Virchow, Berlin; Medical Genetics, Hospital for Sick Children, Toronto; Center for Human and Molecular Genetics, University of Medicine and Dentistry of New Jersey, Newark, NJ; Department of Pediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates; Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands; Clinical Genetics Unit, Birmingham Women’s Healthcare, and Department of Pediatric Endocrinology, Birmingham Children’s Hospital, Birmingham, United Kingdom; Department of Medical Genetics, Hopital Necker, Paris; Genetics Center, Hopital d’Enfants, Dijon, France; Department of Clinical Genetics, Great Ormond Street Hospital, London; Department of Medical Genetics, Ghent University Hospital, Ghent, Belgium; Children’s Hospital, University of Mainz, Mainz, Germany; Department of Genetics, University of São Paulo, São Paulo, Brazil; Department of Clinical Genetics, The Leeds Teaching Hospital, Leeds, United Kingdom; and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore
| | - Jeremy Kirk
- Departments of Genetics, Epidemiology and Biostatistics, Biochemistry, and Pediatrics, Case Western Reserve University School of Medicine, Center for Human Genetics, University Hospitals of Cleveland, and Department of Pediatrics, Metro Health Medical Center, Cleveland; Department of Human Genetics, University Medical Centre Nijmegen, Nijmegen, The Netherlands; Departments of Pediatrics and Medical Genetics, University of Wisconsin–Madison, Madison, WI; Institut für Medizinische Genetik Charité, Campus Virchow, Berlin; Medical Genetics, Hospital for Sick Children, Toronto; Center for Human and Molecular Genetics, University of Medicine and Dentistry of New Jersey, Newark, NJ; Department of Pediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates; Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands; Clinical Genetics Unit, Birmingham Women’s Healthcare, and Department of Pediatric Endocrinology, Birmingham Children’s Hospital, Birmingham, United Kingdom; Department of Medical Genetics, Hopital Necker, Paris; Genetics Center, Hopital d’Enfants, Dijon, France; Department of Clinical Genetics, Great Ormond Street Hospital, London; Department of Medical Genetics, Ghent University Hospital, Ghent, Belgium; Children’s Hospital, University of Mainz, Mainz, Germany; Department of Genetics, University of São Paulo, São Paulo, Brazil; Department of Clinical Genetics, The Leeds Teaching Hospital, Leeds, United Kingdom; and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore
| | - Geert R. Mortier
- Departments of Genetics, Epidemiology and Biostatistics, Biochemistry, and Pediatrics, Case Western Reserve University School of Medicine, Center for Human Genetics, University Hospitals of Cleveland, and Department of Pediatrics, Metro Health Medical Center, Cleveland; Department of Human Genetics, University Medical Centre Nijmegen, Nijmegen, The Netherlands; Departments of Pediatrics and Medical Genetics, University of Wisconsin–Madison, Madison, WI; Institut für Medizinische Genetik Charité, Campus Virchow, Berlin; Medical Genetics, Hospital for Sick Children, Toronto; Center for Human and Molecular Genetics, University of Medicine and Dentistry of New Jersey, Newark, NJ; Department of Pediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates; Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands; Clinical Genetics Unit, Birmingham Women’s Healthcare, and Department of Pediatric Endocrinology, Birmingham Children’s Hospital, Birmingham, United Kingdom; Department of Medical Genetics, Hopital Necker, Paris; Genetics Center, Hopital d’Enfants, Dijon, France; Department of Clinical Genetics, Great Ormond Street Hospital, London; Department of Medical Genetics, Ghent University Hospital, Ghent, Belgium; Children’s Hospital, University of Mainz, Mainz, Germany; Department of Genetics, University of São Paulo, São Paulo, Brazil; Department of Clinical Genetics, The Leeds Teaching Hospital, Leeds, United Kingdom; and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore
| | - Jules Leroy
- Departments of Genetics, Epidemiology and Biostatistics, Biochemistry, and Pediatrics, Case Western Reserve University School of Medicine, Center for Human Genetics, University Hospitals of Cleveland, and Department of Pediatrics, Metro Health Medical Center, Cleveland; Department of Human Genetics, University Medical Centre Nijmegen, Nijmegen, The Netherlands; Departments of Pediatrics and Medical Genetics, University of Wisconsin–Madison, Madison, WI; Institut für Medizinische Genetik Charité, Campus Virchow, Berlin; Medical Genetics, Hospital for Sick Children, Toronto; Center for Human and Molecular Genetics, University of Medicine and Dentistry of New Jersey, Newark, NJ; Department of Pediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates; Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands; Clinical Genetics Unit, Birmingham Women’s Healthcare, and Department of Pediatric Endocrinology, Birmingham Children’s Hospital, Birmingham, United Kingdom; Department of Medical Genetics, Hopital Necker, Paris; Genetics Center, Hopital d’Enfants, Dijon, France; Department of Clinical Genetics, Great Ormond Street Hospital, London; Department of Medical Genetics, Ghent University Hospital, Ghent, Belgium; Children’s Hospital, University of Mainz, Mainz, Germany; Department of Genetics, University of São Paulo, São Paulo, Brazil; Department of Clinical Genetics, The Leeds Teaching Hospital, Leeds, United Kingdom; and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore
| | - Bernhard Zabel
- Departments of Genetics, Epidemiology and Biostatistics, Biochemistry, and Pediatrics, Case Western Reserve University School of Medicine, Center for Human Genetics, University Hospitals of Cleveland, and Department of Pediatrics, Metro Health Medical Center, Cleveland; Department of Human Genetics, University Medical Centre Nijmegen, Nijmegen, The Netherlands; Departments of Pediatrics and Medical Genetics, University of Wisconsin–Madison, Madison, WI; Institut für Medizinische Genetik Charité, Campus Virchow, Berlin; Medical Genetics, Hospital for Sick Children, Toronto; Center for Human and Molecular Genetics, University of Medicine and Dentistry of New Jersey, Newark, NJ; Department of Pediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates; Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands; Clinical Genetics Unit, Birmingham Women’s Healthcare, and Department of Pediatric Endocrinology, Birmingham Children’s Hospital, Birmingham, United Kingdom; Department of Medical Genetics, Hopital Necker, Paris; Genetics Center, Hopital d’Enfants, Dijon, France; Department of Clinical Genetics, Great Ormond Street Hospital, London; Department of Medical Genetics, Ghent University Hospital, Ghent, Belgium; Children’s Hospital, University of Mainz, Mainz, Germany; Department of Genetics, University of São Paulo, São Paulo, Brazil; Department of Clinical Genetics, The Leeds Teaching Hospital, Leeds, United Kingdom; and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore
| | - Chong Ae Kim
- Departments of Genetics, Epidemiology and Biostatistics, Biochemistry, and Pediatrics, Case Western Reserve University School of Medicine, Center for Human Genetics, University Hospitals of Cleveland, and Department of Pediatrics, Metro Health Medical Center, Cleveland; Department of Human Genetics, University Medical Centre Nijmegen, Nijmegen, The Netherlands; Departments of Pediatrics and Medical Genetics, University of Wisconsin–Madison, Madison, WI; Institut für Medizinische Genetik Charité, Campus Virchow, Berlin; Medical Genetics, Hospital for Sick Children, Toronto; Center for Human and Molecular Genetics, University of Medicine and Dentistry of New Jersey, Newark, NJ; Department of Pediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates; Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands; Clinical Genetics Unit, Birmingham Women’s Healthcare, and Department of Pediatric Endocrinology, Birmingham Children’s Hospital, Birmingham, United Kingdom; Department of Medical Genetics, Hopital Necker, Paris; Genetics Center, Hopital d’Enfants, Dijon, France; Department of Clinical Genetics, Great Ormond Street Hospital, London; Department of Medical Genetics, Ghent University Hospital, Ghent, Belgium; Children’s Hospital, University of Mainz, Mainz, Germany; Department of Genetics, University of São Paulo, São Paulo, Brazil; Department of Clinical Genetics, The Leeds Teaching Hospital, Leeds, United Kingdom; and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore
| | - Yanick Crow
- Departments of Genetics, Epidemiology and Biostatistics, Biochemistry, and Pediatrics, Case Western Reserve University School of Medicine, Center for Human Genetics, University Hospitals of Cleveland, and Department of Pediatrics, Metro Health Medical Center, Cleveland; Department of Human Genetics, University Medical Centre Nijmegen, Nijmegen, The Netherlands; Departments of Pediatrics and Medical Genetics, University of Wisconsin–Madison, Madison, WI; Institut für Medizinische Genetik Charité, Campus Virchow, Berlin; Medical Genetics, Hospital for Sick Children, Toronto; Center for Human and Molecular Genetics, University of Medicine and Dentistry of New Jersey, Newark, NJ; Department of Pediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates; Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands; Clinical Genetics Unit, Birmingham Women’s Healthcare, and Department of Pediatric Endocrinology, Birmingham Children’s Hospital, Birmingham, United Kingdom; Department of Medical Genetics, Hopital Necker, Paris; Genetics Center, Hopital d’Enfants, Dijon, France; Department of Clinical Genetics, Great Ormond Street Hospital, London; Department of Medical Genetics, Ghent University Hospital, Ghent, Belgium; Children’s Hospital, University of Mainz, Mainz, Germany; Department of Genetics, University of São Paulo, São Paulo, Brazil; Department of Clinical Genetics, The Leeds Teaching Hospital, Leeds, United Kingdom; and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore
| | - Nancy E. Braverman
- Departments of Genetics, Epidemiology and Biostatistics, Biochemistry, and Pediatrics, Case Western Reserve University School of Medicine, Center for Human Genetics, University Hospitals of Cleveland, and Department of Pediatrics, Metro Health Medical Center, Cleveland; Department of Human Genetics, University Medical Centre Nijmegen, Nijmegen, The Netherlands; Departments of Pediatrics and Medical Genetics, University of Wisconsin–Madison, Madison, WI; Institut für Medizinische Genetik Charité, Campus Virchow, Berlin; Medical Genetics, Hospital for Sick Children, Toronto; Center for Human and Molecular Genetics, University of Medicine and Dentistry of New Jersey, Newark, NJ; Department of Pediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates; Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands; Clinical Genetics Unit, Birmingham Women’s Healthcare, and Department of Pediatric Endocrinology, Birmingham Children’s Hospital, Birmingham, United Kingdom; Department of Medical Genetics, Hopital Necker, Paris; Genetics Center, Hopital d’Enfants, Dijon, France; Department of Clinical Genetics, Great Ormond Street Hospital, London; Department of Medical Genetics, Ghent University Hospital, Ghent, Belgium; Children’s Hospital, University of Mainz, Mainz, Germany; Department of Genetics, University of São Paulo, São Paulo, Brazil; Department of Clinical Genetics, The Leeds Teaching Hospital, Leeds, United Kingdom; and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore
| | - Focco van den Akker
- Departments of Genetics, Epidemiology and Biostatistics, Biochemistry, and Pediatrics, Case Western Reserve University School of Medicine, Center for Human Genetics, University Hospitals of Cleveland, and Department of Pediatrics, Metro Health Medical Center, Cleveland; Department of Human Genetics, University Medical Centre Nijmegen, Nijmegen, The Netherlands; Departments of Pediatrics and Medical Genetics, University of Wisconsin–Madison, Madison, WI; Institut für Medizinische Genetik Charité, Campus Virchow, Berlin; Medical Genetics, Hospital for Sick Children, Toronto; Center for Human and Molecular Genetics, University of Medicine and Dentistry of New Jersey, Newark, NJ; Department of Pediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates; Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands; Clinical Genetics Unit, Birmingham Women’s Healthcare, and Department of Pediatric Endocrinology, Birmingham Children’s Hospital, Birmingham, United Kingdom; Department of Medical Genetics, Hopital Necker, Paris; Genetics Center, Hopital d’Enfants, Dijon, France; Department of Clinical Genetics, Great Ormond Street Hospital, London; Department of Medical Genetics, Ghent University Hospital, Ghent, Belgium; Children’s Hospital, University of Mainz, Mainz, Germany; Department of Genetics, University of São Paulo, São Paulo, Brazil; Department of Clinical Genetics, The Leeds Teaching Hospital, Leeds, United Kingdom; and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore
| | - Matthew L. Warman
- Departments of Genetics, Epidemiology and Biostatistics, Biochemistry, and Pediatrics, Case Western Reserve University School of Medicine, Center for Human Genetics, University Hospitals of Cleveland, and Department of Pediatrics, Metro Health Medical Center, Cleveland; Department of Human Genetics, University Medical Centre Nijmegen, Nijmegen, The Netherlands; Departments of Pediatrics and Medical Genetics, University of Wisconsin–Madison, Madison, WI; Institut für Medizinische Genetik Charité, Campus Virchow, Berlin; Medical Genetics, Hospital for Sick Children, Toronto; Center for Human and Molecular Genetics, University of Medicine and Dentistry of New Jersey, Newark, NJ; Department of Pediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates; Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands; Clinical Genetics Unit, Birmingham Women’s Healthcare, and Department of Pediatric Endocrinology, Birmingham Children’s Hospital, Birmingham, United Kingdom; Department of Medical Genetics, Hopital Necker, Paris; Genetics Center, Hopital d’Enfants, Dijon, France; Department of Clinical Genetics, Great Ormond Street Hospital, London; Department of Medical Genetics, Ghent University Hospital, Ghent, Belgium; Children’s Hospital, University of Mainz, Mainz, Germany; Department of Genetics, University of São Paulo, São Paulo, Brazil; Department of Clinical Genetics, The Leeds Teaching Hospital, Leeds, United Kingdom; and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore
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32
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Masson P, Nachon F, Bartels CF, Froment MT, Ribes F, Matthews C, Lockridge O. High activity of human butyrylcholinesterase at low pH in the presence of excess butyrylthiocholine. Eur J Biochem 2003; 270:315-24. [PMID: 12605682 DOI: 10.1046/j.1432-1033.2003.03388.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Butyrylcholinesterase is a serine esterase, closely related to acetylcholinesterase. Both enzymes employ a catalytic triad mechanism for catalysis, similar to that used by serine proteases such as alpha-chymotrypsin. Enzymes of this type are generally considered to be inactive at pH values below 5, because the histidine member of the catalytic triad becomes protonated. We have found that butyrylcholinesterase retains activity at pH <or= 5, under conditions of excess substrate activation. This low-pH activity appears with wild-type butyrylcholinesterase as well as with all mutants we examined: A328G, A328I, A328F, A328Y, A328W, E197Q, L286W, V288W and Y332A (residue A328 is at the bottom of the active-site gorge, near the pi-cation-binding site; E197 is next to the active-site serine S198; L286 and V288 form the acyl-binding pocket; and Y332 is a component of the peripheral anionic site). For example, the kcat value at pH 5.0 for activity in the presence of excess substrate was 32900 +/- 4400 min(-1) for wild-type, 55200 +/- 1600 min(-1) for A328F, and 28 700 +/- 700 min(-1) for A328W. This activity is titratable, with pKa values of 6.0-6.6, suggesting that the catalytic histidine is protonated at pH 5. The existence of activity when the catalytic histidine is protonated indicates that the catalytic-triad mechanism of butyrylcholinesterase does not operate for catalysis at low pH. The mechanism explaining the catalytic behaviour of butyrylcholinesterase at low pH in the presence of excess substrate remains to be elucidated.
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Affiliation(s)
- Patrick Masson
- Centre de Recherches du Service de Santé des Armées, Unité d'Enzymologie, La Tronche, France.
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Everman DB, Bartels CF, Yang Y, Yanamandra N, Goodman FR, Mendoza-Londono JR, Savarirayan R, White SM, Graham JM, Gale RP, Svarch E, Newman WG, Kleckers AR, Francomano CA, Govindaiah V, Singh L, Morrison S, Thomas JT, Warman ML. The mutational spectrum of brachydactyly type C. Am J Med Genet 2002; 112:291-6. [PMID: 12357473 DOI: 10.1002/ajmg.10777] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Growth/differentiation factor-5 (GDF5), also known as cartilage-derived morphogenetic protein-1 (CDMP-1), is a secreted signaling molecule that participates in skeletal morphogenesis. Heterozygous mutations in GDF5, which maps to human chromosome 20, occur in individuals with autosomal dominant brachydactyly type C (BDC). Here we show that BDC is locus homogeneous by reporting a GDF5 frameshift mutation segregating with the phenotype in a family whose trait was initially thought to map to human chromosome 12. We also describe heterozygous mutations in nine additional probands/families with BDC and show nonpenetrance in a mutation carrier. Finally, we show that mutant GDF5 polypeptides containing missense mutations in their active domains do not efficiently form disulfide-linked dimers when expressed in vitro. These data support the hypothesis that BDC results from functional haploinsufficiency for GDF5.
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Affiliation(s)
- David B Everman
- Department of Genetics, Case Western Reserve University, Cleveland, Ohio 44106, USA
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Duysen EG, Bartels CF, Lockridge O. Wild-type and A328W mutant human butyrylcholinesterase tetramers expressed in Chinese hamster ovary cells have a 16-hour half-life in the circulation and protect mice from cocaine toxicity. J Pharmacol Exp Ther 2002; 302:751-8. [PMID: 12130740 DOI: 10.1124/jpet.102.033746] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Human butyrylcholinesterase (BChE) hydrolyzes cocaine to inactive metabolites. A mutant of human BChE, A328W, hydrolyzed cocaine 15-fold faster compared with wild-type BChE. Although the catalytic properties of human BChE secreted by Chinese hamster ovary (CHO) cells are identical to those of native BChE, a major difference became evident when the recombinant BChE was injected into rats and mice. Recombinant BChE disappeared from the circulation within minutes, whereas native BChE stayed in the blood for a week. Nondenaturing gel electrophoresis showed that the recombinant BChE consisted mainly of monomers and dimers. In contrast, native BChE is a tetramer. The problem of the short residence time was solved by finding a method to assemble the recombinant BChE into tetramers. Coexpression in CHO cells of BChE and 45 residues from the N terminus of the COLQ protein yielded 70% tetrameric BChE. The resulting purified recombinant BChE tetramers had a half-life of 16 h in the circulation of rats and mice. The 16-h half-life was achieved without modifying the carbohydrate content of recombinant BChE. The protective effect of recombinant wild-type and A328W mutant BChE against cocaine toxicity was tested by measuring locomotor activity in mice. Pretreatment with wild-type BChE or A328W tetramers at a dose of 2.8 units/g i.p. reduced cocaine-induced locomotor activity by 50 and 80%. These results indicate that recombinant human BChE could be useful for treating cocaine toxicity in humans.
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Affiliation(s)
- Ellen G Duysen
- Eppley Institute, University of Nebraska Medical Center, 986806 Nebraska Medical Center, Omaha, NE 68198-6805, USA
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Masson P, Schopfer LM, Bartels CF, Froment MT, Ribes F, Nachon F, Lockridge O. Substrate activation in acetylcholinesterase induced by low pH or mutation in the pi-cation subsite. Biochim Biophys Acta 2002; 1594:313-24. [PMID: 11904227 DOI: 10.1016/s0167-4838(01)00323-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Substrate inhibition is considered a defining property of acetylcholinesterase (AChE), whereas substrate activation is characteristic of butyrylcholinesterase (BuChE). To understand the mechanism of substrate inhibition, the pH dependence of acetylthiocholine hydrolysis by AChE was studied between pH 5 and 8. Wild-type human AChE and its mutants Y337G and Y337W, as well as wild-type Bungarus fasciatus AChE and its mutants Y333G, Y333A and Y333W were studied. The pH profile results were unexpected. Instead of substrate inhibition, wild-type AChE and all mutants showed substrate activation at low pH. At high pH, there was substrate inhibition for wild-type AChE and for the mutant with tryptophan in the pi-cation subsite, but substrate activation for mutants containing small residues, glycine or alanine. This is particularly apparent in the B. fasciatus AChE. Thus a single amino acid substitution in the pi-cation site, from the aromatic tyrosine of B. fasciatus AChE to the alanine of BuChE, caused AChE to behave like BuChE. Excess substrate binds to the peripheral anionic site (PAS) of AChE. The finding that AChE is activated by excess substrate supports the idea that binding of a second substrate molecule to the PAS induces a conformational change that reorganizes the active site.
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Affiliation(s)
- Patrick Masson
- Centre de Recherches du Service de Santé des Armées, Unité d'Enzymologie, La Tronche Cédex, france.
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Abstract
Ideally we would like to treat people exposed to nerve agents with an enzyme that rapidly destroys nerve agents. The enzymes considered for such a role include human butyrylcholinesterase (BChE), acetylcholinesterase (AChE), carboxylesterase and paraoxonase (PON1). Success has been achieved in endowing BChE with the ability to hydrolyze organophosphates. The G117H mutant of BCHE hydrolyzes sarin and VX, whereas the double mutant G117H/E197Q hydrolyzes soman (Millard et al. Biochemistry 1995; 34: 15925-15933; 1998; 37: 237-247). However, the rates of organophosphate hydrolysis are slow and a faster organophosphate hydrolase is being sought. Native PON1 hydrolyzes paraoxon with a catalytic efficiency, of 2.4 x 10(6) M(-1) x min(-1), and our goal is to improve the organophosphate hydrolase activity of PON1. To achieve this we need to identify the amino acids in the active site of PON1. Using site-directed mutagenesis and expression in human 293T cells, we have identified the following eight amino acids as being essential to PON1 activity: W280, H114, H133, H154, H242, H284, E52 and D53. Fluorescence of PON1 complexed to terbium ion shows that at least one tryptophan is close to the calcium binding site.
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Affiliation(s)
- D Josse
- University of Nebraska Medical Center, Eppley Institute, Omaha, NE 68198-6805, USA
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Bartels CF, Xie W, Miller-Lindholm AK, Schopfer LM, Lockridge O. Determination of the DNA sequences of acetylcholinesterase and butyrylcholinesterase from cat and demonstration of the existence of both in cat plasma. Biochem Pharmacol 2000; 60:479-87. [PMID: 10874122 DOI: 10.1016/s0006-2952(00)00365-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Cat serum contains 0.5 mg/L of butyrylcholinesterase (BChE, EC 3.1.1. 8) and 0.3 mg/L of acetylcholinesterase (AChE, EC 3.1.1.7); this can be compared with 5 mg/mL and < 0.01 mg/L, respectively, in human serum. Cat BChE differed from human BChE in the steady-state turnover of butyrylthiocholine, having a 3-fold higher k(cat) and 2-fold higher K(m) and K(ss) values. Sequencing of the cat BCHE cDNA revealed 70 amino acid differences between cat and human BChE, three of which could account for these kinetic differences. These amino acids, which were located in the region of the active site, were Phe398Ile, Pro285Leu, and Ala277Leu (where the first amino acid was found in human and the second in cat). Sequencing genomic DNA for cat and human ACHE demonstrated that there were 33 amino acid differences between the cat and human AChE enzymes, but that there were no differences in the active site region. In addition, a polymorphism in intron 3 of the human ACHE gene was detected, as well as a silent polymorphism at Y116 of the cat ACHE gene.
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Affiliation(s)
- C F Bartels
- Eppley Institute, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA.
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Altamirano CV, Bartels CF, Lockridge O. The butyrylcholinesterase K-variant shows similar cellular protein turnover and quaternary interaction to the wild-type enzyme. J Neurochem 2000; 74:869-77. [PMID: 10646540 DOI: 10.1046/j.1471-4159.2000.740869.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A recent study has linked the butyrylcholinesterase (BChE) K-variant and the apolipoprotein epsilon4 isoform to late-onset Alzheimer's disease. These findings have been controversial and have led us to examine the differences between wild-type and K-variant BChE in enzyme activity, protein stability, and quaternary structure. J-variant BChE (E497V/A539T) was also studied because it is associated with the K-variant mutation. The K-variant mutation (A539T) is located in the C-terminal tetramerization domain. Wild-type, K-variant, and J-variant BChE were expressed in Chinese hamster ovary cells and purified. The purified enzymes had similar binding affinity (Km) values and catalytic rates for butyrylthiocholine and benzoylcholine. In pulse-chase studies the K-variant, J-variant, and wildtype BChE were degraded rapidly within the cell, with a half-time of approximately 1.5 h. Less than 5% of the intracellular BChE was exported. The C-terminal peptide containing the K-variant mutation interacted with itself as strongly as did the wild-type peptide in the yeast two-hybrid system. Both K-variant and wild-type BChE assembled into tetramers in the presence of poly-L-proline or the proline-rich attachment domain of the collagen tail. The native K-variant BChE in serum showed the same proportion of tetramers as the native serum wild-type BChE. We conclude that the K-variant BChE is similar to wild-type BChE in enzyme activity, protein turnover, and tetramer formation.
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Affiliation(s)
- C V Altamirano
- Department of Biochemistry and Molecular Biology and Eppley Institute, University of Nebraska Medical Center, Omaha 68198-6805, USA
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39
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Miller-Lindholm AK, Bedows E, Bartels CF, Ramey J, Maclin V, Ruddon RW. A naturally occurring genetic variant in the human chorionic gonadotropin-beta gene 5 is assembly inefficient. Endocrinology 1999; 140:3496-506. [PMID: 10433205 DOI: 10.1210/endo.140.8.6915] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The hCGbeta gene family is composed of six homologous genes linked in tandem repeat on chromosome 19; the order of the genes is 7, 8, 5, 1, 2, and 3. Previous studies have shown that hCGbeta gene 5 is highly expressed during the first trimester of pregnancy. The purpose of our study was to identify naturally occurring polymorphisms in hCGbeta gene 5 and determine whether these alterations affected hCG function. The data presented here show that hCGbeta gene 5 was highly conserved in the 334 asymptomatic individuals and 41 infertile patients examined for polymorphisms using PCR followed by single stranded conformational polymorphism analysis. Most of the polymorphisms detected were either silent or located in intron regions. However, one genetic variant identified in beta gene 5 exon 3 was a G to A transition that changed the naturally occurring valine residue to methionine in codon 79 (V79M) in 4.2% of the random population studied. The V79M polymorphism was always linked to a silent C to T transition in codon 82 (tyrosine). To determine whether betaV79M hCG had biological properties that differed from those of wild-type hCG, a beta-subunit containing the V79M substitution was created by site-directed mutagenesis and was coexpressed with the glycoprotein hormone alpha-subunit in Chinese hamster ovary cells and 293T cells. When we examined betaV79M hCG biosynthesis, we detected atypical betaV79M hCG folding intermediates, including a betaV79M conformational variant that resulted in a beta-subunit with impaired ability to assemble with the alpha-subunit. The inefficient assembly of betaV79M hCG appeared to be independent of beta-subunit glycosylation or of the cell type studied, but, rather, was due to the inability of the betaV79M subunit to fold correctly. The majority of the V79M beta-subunit synthesized was secreted as unassembled free beta. Although the amount of alphabeta hCG heterodimer formed and secreted by betaV79M-producing cells was less than that by wild-type beta-producing cells, the hCG that was secreted as alphabeta V79M heterodimer exhibited biological activity indistinguishable from that of wild-type hCG.
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MESH Headings
- Abortion, Spontaneous/genetics
- Amino Acid Substitution
- Animals
- CHO Cells
- Cell Line
- Chorionic Gonadotropin, beta Subunit, Human/biosynthesis
- Chorionic Gonadotropin, beta Subunit, Human/chemistry
- Chorionic Gonadotropin, beta Subunit, Human/genetics
- Chromosome Mapping
- Chromosomes, Human, Pair 19
- Cricetinae
- DNA/blood
- DNA/genetics
- Female
- Genetic Variation
- Glycoprotein Hormones, alpha Subunit/chemistry
- Humans
- Infertility, Female/genetics
- Male
- Methionine
- Models, Molecular
- Multigene Family
- Mutagenesis, Site-Directed
- Point Mutation
- Polymorphism, Single-Stranded Conformational
- Pregnancy
- Protein Structure, Secondary
- Recombinant Proteins/biosynthesis
- Transfection
- Valine
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Affiliation(s)
- A K Miller-Lindholm
- Eppley Institute for Research in Cancer and Allied Diseases, Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha 68198-6805, USA
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Xie W, Altamirano CV, Bartels CF, Speirs RJ, Cashman JR, Lockridge O. An improved cocaine hydrolase: the A328Y mutant of human butyrylcholinesterase is 4-fold more efficient. Mol Pharmacol 1999; 55:83-91. [PMID: 9882701 DOI: 10.1124/mol.55.1.83] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Butyrylcholinesterase (BChE) has a major role in cocaine detoxication. The rate at which human BChE hydrolyzes cocaine is slow, with a kcat of 3.9 min(-1) and Km of 14 microM. Our goal was to improve cocaine hydrolase activity by mutating residues near the active site. The mutant A328Y had a kcat of 10.2 min(-1) and Km of 9 microM for a 4-fold improvement in catalytic efficiency (kcat/Km). Since benzoylcholine (kcat 15,000 min(-1)) and cocaine form the same acyl-enzyme intermediate but are hydrolyzed at 4000-fold different rates, it was concluded that a step leading to formation of the acyl-enzyme intermediate was rate-limiting. BChE purified from plasma of cat, horse, and chicken was tested for cocaine hydrolase activity. Compared with human BChE, horse BChE had a 2-fold higher kcat but a lower binding affinity, cat BChE was similar to human, and chicken BChE had only 10% of the catalytic efficiency. Naturally occurring genetic variants of human BChE were tested for cocaine hydrolase activity. The J and K variants (E497V and A539T) had k(cat) and Km values similar to wild-type, but because these variants are reduced to 66 and 33% of normal levels in human blood, respectively, people with these variants may be at risk for cocaine toxicity. The atypical variant (D70G) had a 10-fold lower binding affinity for cocaine, suggesting that persons with the atypical variant of BChE may experience severe or fatal cocaine intoxication when administered a dose of cocaine that is not harmful to others.
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Affiliation(s)
- W Xie
- Eppley Institute and Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68198-6805, USA
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Vanlinthout LE, Bartels CF, Lockridge O, Callens K, Booij LH. Prolonged Paralysis After a Test Dose of Mivacurium in a Patient with Atypical Serum Cholinesterase. Anesth Analg 1998. [DOI: 10.1213/00000539-199811000-00042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Vanlinthout LE, Bartels CF, Lockridge O, Callens K, Booij LH. Prolonged paralysis after a test dose of mivacurium in a patient with atypical serum cholinesterase. Anesth Analg 1998; 87:1199-202. [PMID: 9806709 DOI: 10.1097/00000539-199811000-00042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- L E Vanlinthout
- Institute for Anesthesiology, Academic Hospital Nijmegen, The Netherlands
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Masson P, Froment MT, Fortier PL, Visicchio JE, Bartels CF, Lockridge O. Butyrylcholinesterase-catalysed hydrolysis of aspirin, a negatively charged ester, and aspirin-related neutral esters. Biochim Biophys Acta 1998; 1387:41-52. [PMID: 9748494 DOI: 10.1016/s0167-4838(98)00104-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Although aspirin (acetylsalicylic acid) is negatively charged, it is hydrolysed by butyrylcholinesterase (BuChE). Catalytic parameters were determined in 100 mM Tris buffer, pH 7.4, in the presence and absence of metal cations. The presence of Ca2+ or Mg2+ (<100 mM) in buffer did not change the Km, but accelerated the rate of hydrolysis of aspirin by wild-type or D70G mutant BuChE by 5-fold. Turnover numbers were of the order of 5000-12000 min-1 for the wild-type enzyme and the D70G and D70K enzymes in 100 mM Tris, pH 7.4, containing 50 mM CaCl2 at 25 degreesC; Km values were 6 mM for wild-type, 16 mM for D70G and 38 mM for D70K. People with 'atypical' BuChE have the D70G mutation. The apparent inhibition seen at high aspirin concentration was not due to inhibition by excess substrate but to spontaneous hydrolysis of aspirin, causing inhibition by salicylate. The wild-type and D70G enzymes were competitively inhibited by salicylic acid; the D70K enzyme showed a complex parabolic inhibition, suggesting multiple binding. The effect of salicylate was substrate-dependent, the D70K mutant being activated by salicylate with butyrylthiocholine as substrate. Km value for wild-type enzyme was lower than for D70 mutants, suggesting that residue 70 located at the rim of the active site gorge was not the major site for the initial encounter aspirin-BuChE complex. On the other hand, the virtual absence of affinity of the W82A mutant for aspirin indicated that W82 was the major residue involved in formation of the Michaelis complex. Molecular modelling of aspirin binding to BuChE indicated perpendicular interactions between the aromatic rings of W82 and aspirin. Kinetic study of BuChE-catalysed hydrolysis of different acetyl esters showed that the rate limiting step was acetylation. The bimolecular rate constants for hydrolysis of aspirin by wild-type, D70G and D70K enzymes were found to be close to 1x106 M-1 min-1. These results support the contention that the electrostatic steering due to the negative electrostatic field of the enzyme plays a role in substrate binding, but plays no role in the catalytic steps, i.e. in the enzyme acetylation.
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Affiliation(s)
- P Masson
- Centre de Recherches du Service de Santé des Armées, Unité d'Enzymologie, 24 av. des Maquis du Grésivaudan, B.P. 87, 38702 La Tronche Cedex, France
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Abstract
Organophosphate-inhibited cholinesterases can be reactivated by nucleophilic compounds. Sometimes phosphylated (phosphorylated or phosphonylated) cholinesterases become progressively refractory to reactivation; this can result from different reactions. The most frequent process, termed 'aging', involves the dealkylation of an alkoxy group on the phosphyl moiety through a carbocation mechanism. In attempting to determine the amino acid residues involved in the aging of butyrylcholinesterase (BuChE), the human BuChE gene was mutated at several positions corresponding to residues located at the rim of the active site gorge and in the vicinity of the active site. Mutant enzymes were expressed in Chinese hamster ovary cells. Wild-type BuChE and mutants were inhibited by di-isopropylfluorophosphate at pH 8.0 and 25 degrees C. Di-isopropyl-phosphorylated enzymes were incubated with the nucleophilic oxime 2-pyridine aldoxime methiodide and their reactivatability was determined. Reactivatability was expressed by the first-order rate constant of aging and/or the half-life of aging (t12). The t12 was found to be of the order of 60 min for wild-type BuChE. Mutations on Glu-197 increased t12 60-fold. Mutation W82A increased t12 13-fold. Mutation D70G increased t12 8-fold. Mutations in the vicinity of the active site serine residue had either moderate or no effect on aging; t12 was doubled for F329C and F329A, increased only 4-fold for the double mutant A328G+F329S, and no change was observed for the A328G mutant, indicating that the isopropoxy chain to be dealkylated does not directly interact with Ala-328 and Phe-329. These results were interpreted by molecular modelling of di-isopropylphosphorylated wild-type and mutant enzymes. Molecular dynamics simulations indicated that the isopropyl chain that is lost interacted with Trp-82, suggesting that Trp-82 has a role in stabilizing the carbonium ion that is released in the dealkylation step. This study emphasized the important role of the Glu-197 carboxylate in stabilizing the developing carbocation, and the allosteric control of the dealkylation reaction by Asp-70. Indeed, although Asp-70 does not interact with the phosphoryl moiety, mutation D70G affects the rate of aging. This indirect control was interpreted in terms of change in the conformational state of Trp-82 owing to internal motions of the Omega loop (Cys-65-Cys-92) in the mutant enzyme.
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Affiliation(s)
- P Masson
- Centre de Recherches du Service de Santé des Armées, Unité de Biochimie, 24 avenue des Maquis du Grésivaudan, B.P. 87, 38702 La Tronche Cédex, France
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Masson P, Froment MT, Bartels CF, Lockridge O. Importance of aspartate-70 in organophosphate inhibition, oxime re-activation and aging of human butyrylcholinesterase. Biochem J 1997; 325 ( Pt 1):53-61. [PMID: 9224629 PMCID: PMC1218528 DOI: 10.1042/bj3250053] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.0] [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: 02/04/2023]
Abstract
Asp-70 is the defining amino acid in the peripheral anionic site of human butyrylcholinesterase (BuChE), whereas acetylcholinesterase has several additional amino acids, the most important one being Trp-277 (Trp-279 in Torpedo AChE). We studied mutants D70G, D70K and A277W to evaluate the role of Asp-70 and Trp-277 in reactions with organophosphates. We found that Asp-70 was important for binding positively charged echothiophate, but not neutral paraoxon and iso-OMPA. Asp-70 was also important for binding of positively charged pralidoxime (2-PAM) and for activation of re-activation by excess 2-PAM. Excess 2-PAM had an effect similar to substrate activation, suggesting the binding of 2 mol of 2-PAM to wild-type but not to the D70G mutant. A surprising result was that Asp-70 was important for irreversible aging, the D70G mutant having a 3- and 8-fold lower rate of aging for paraoxon-inhibited and di-isopropyl fluorophosphate-inhibited BuChE. Mutants of Asp-70 had the same rate constants for phosphorylation and re-activation by 2-PAM as wild-type. The A277W mutant behaved like wild-type in all assays. Our results predict that people with the atypical (D70G) variant of BuChE will be more sensitive to the toxic effects of echothiophate, but will be equally sensitive to paraoxon and di-isopropyl fluorophosphate. People with the D70G mutation will be resistant to re-activation of their inhibited BuChE by 2-PAM, but this will be offset by the lower rate of irreversible aging of inhibited BuChE, allowing some regeneration by spontaneous hydrolysis.
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Affiliation(s)
- P Masson
- Centre de Recherches du Service de Santé des Armées, Unité de Biochimie, BP 87, 38702 La Tronche Cédex, France and Eppley Institute, University of Nebraska Medical Center, Omaha, NE 68198-6805, USA
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Masson P, Legrand P, Bartels CF, Froment MT, Schopfer LM, Lockridge O. Role of aspartate 70 and tryptophan 82 in binding of succinyldithiocholine to human butyrylcholinesterase. Biochemistry 1997; 36:2266-77. [PMID: 9047329 DOI: 10.1021/bi962484a] [Citation(s) in RCA: 116] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The atypical variant of human butyrylcholinesterase has Gly in place of Asp 70. Patients with this D70G mutation respond abnormally to the muscle relaxant succinyldicholine, experiencing hours of apnea rather than the intended 3 min. Asp 70 is at the rim of the active site gorge 12 A from the active site Ser 198. An unanswered question in the literature is why the atypical variant has a 10-fold increase in Km for compounds with a single positive charge but a 100-fold increase in Km for compounds with two positive charges. We mutated residues Asp 70, Trp 82, Trp 231, Glu 197, and Tyr 332 and expressed mutant enzymes in mammalian cells. Steady-state kinetic parameters for hydrolysis of butyrylthiocholine, benzoylcholine, succinyldithiocholine, and o-nitrophenyl butyrate were determined. The wild type and the D70G mutant had identical k(cat) values for all substrates. Molecular modeling and molecular dynamics suggested that succinyldicholine could bind in two consecutive orientations in the active site gorge; formation of one complex caused a conformational change in the omega loop involving Asp 70 and Trp 82. We propose the formation of three enzyme-substrate intermediates preceding the acyl-enzyme intermediate; kinetic data support this contention. Substrates with a single positive charge interact with Asp 70 just once, whereas substrates with two positive charges, for example succinyldithiocholine, interact with Asp 70 in two complexes, thus explaining the 10- and 100-fold increases in Km in the D70G mutant.
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Affiliation(s)
- P Masson
- Unité de Biochimie, Centre de Recherches du Service de Santé des Armées, La Tronche, France
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Abstract
The goal of this work was to determine what amino acids at the mouth of the active-site gorge are important for the function of human butyrylcholinesterase. Mutants D70G, Q119Y, G283D, A277W, A277H and A277W/G283D were expressed in human embryonal kidney cells and the secreted enzymes were assayed by steady-state kinetics. The result was that only one amino acid, D70 was found to be important for function. When D70 was mutated to G, the same mutation as in the naturally occurring atypical butyrylcholinesterase, the affinity for positively charged substrates and positively charged inhibitors decreased 5-30-fold. The D70G mutant had another striking abnormality in that it was virtually devoid of the phenomenon of substrate activation by excess butyrylthiocholine. Thus, though kcat was the same for wild-type and D70G mutant, being 24000 min(-1) at low butyrylthiocholine concentrations (0.01-0.1 mM), it failed to increase for the D70G mutant at 40 mM butyrylthiocholine, whereas it increased threefold for wild type. The D70G mutant was more sensitive to changes in salt concentration, its catalytic rate decreasing more than that of the wild type. The D70G mutant appeared to have a greater surface negative charge than wild type suggesting that the D70G mutant had a conformation different from that of the wild type. That D70 affects the function of butyrylcholinesterase, together with its location at the mouth of the active-site gorge, supports the hypothesis that D70 is a component of the peripheral anionic site of butyrylcholinesterase. Mutants containing aromatic amino acids at the mouth of the gorge had increased binding affinity for propidium and fasciculin, but unaltered function, suggesting that aromatic amino acids are not important to the function of the peripheral anionic site of butyrylcholinesterase.
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Affiliation(s)
- P Masson
- Centre de Recherches du Service de Santé des Armées, Unité de Biochimie, La Tronche, France
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Primo-Parmo SL, Bartels CF, Wiersema B, van der Spek AF, Innis JW, La Du BN. Characterization of 12 silent alleles of the human butyrylcholinesterase (BCHE) gene. Am J Hum Genet 1996; 58:52-64. [PMID: 8554068 PMCID: PMC1914969] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The silent phenotype of human butyrylcholinesterase (BChE), present in most human populations in frequencies of approximately 1/100,000, is characterized by the complete absence of BChE activity or by activity <10% of the average levels of the usual phenotype. Heterogeneity in this phenotype has been well established at the phenotypic level, but only a few silent BCHE alleles have been characterized at the DNA level. Twelve silent alleles of the human butyrylcholinesterase gene (BCHE) have been identified in 17 apparently unrelated patients who were selected by their increased sensitivity to the muscle relaxant succinylcholine. All of these alleles are characterized by single nucleotide substitutions or deletions leading to distinct changes in the structure of the BChE enzyme molecule. Nine of the nucleotide substitutions result in the replacement of single amino acid residues. Three of these variants, BCHE*33C, BCHE*198G, and BCHE*201T, produce normal amounts of immunoreactive but enzymatically inactive BChE protein in the plasma. The other six amino acid substitutions, encoded by BCHE*37S, BCHE*125F, BCHE*170E, BCHE*471R, and BCHE*518L, seem to cause reduced expression of BChE protein, and their role in determining the silent phenotype was confirmed by expression in cell culture. The other four silent alleles, BCHE*271STOP, BCHE*500STOP, BCHE*FS6, and BCHE*I2E3-8G, encode BChES truncated at their C-terminus because of premature stop codons caused by nucleotide substitutions, a frame shift, or altered splicing. The large number of different silent BCHE alleles found within a relatively small number of patients shows that the heterogeneity of the silent BChE phenotype is high. The characterization of silent BChE variants will be useful in the study of the structure/function relationship for this and other closely related enzymes.
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Affiliation(s)
- S L Primo-Parmo
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor 48109-0572, USA
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Abstract
Cholinesterase inhibitors occur naturally in the calabar bean (eserine), green potatoes (solanine), insect-resistant crab apples, the coca plant (cocaine) and snake venom (fasciculin). There are also synthetic cholinesterase inhibitors, for example man-made insecticides. These inhibitors inactivate acetylcholinesterase and butyrylcholinesterase as well as other targets. From a study of the tissue distribution of acetylcholinesterase and butyrylcholinesterase mRNA by Northern blot analysis, we have found the highest levels of butyrylcholinesterase mRNA in the liver and lungs, tissues known as the principal detoxication sites of the human body. These results indicate that butyrylcholinesterase may be a first line of defense against poisons that are eaten or inhaled.
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Affiliation(s)
- O Jbilo
- Institut National de la Recherche Agronomique, Montpellier, France
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Kris M, Jbilo O, Bartels CF, Masson P, Rhode S, Lockridge O. Endogenous butyrylcholinesterase in SV40 transformed cell lines: COS-1, COS-7, MRC-5 SV40, and WI-38 VA13. In Vitro Cell Dev Biol Anim 1994; 30A:680-9. [PMID: 7842168 DOI: 10.1007/bf02631271] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Comparison of proteins expressed by SV40 transformed cell lines and untransformed cell lines is of interest because SV40 transformed cells are immortal, whereas untransformed cells senesce after about 50 doublings. In MRC-5 SV40 cells, only seven proteins have previously been reported to shift from undetectable to detectable after transformation by SV40 virus. We report that butyrylcholinesterase is an 8th protein in this category. Butyrylcholinesterase activity in transformed MRC-5 SV40 cells increased at least 150-fold over its undetectable level in MRC-5 parental cells. Other SV40 transformed cell lines, including COS-1, COS-7, and WI-38 VA13, also expressed endogenous butyrylcholinesterase, whereas the parental, untransformed cell lines, CV-1 and WI-38, had no detectable butyrylcholinesterase activity or mRNA. Infection of CV-1 cells by SV40 virus did not result in expression of butyrylcholinesterase, showing that the butyrylcholinesterase promoter was not activated by the large T antigen of SV40. We conclude that butyrylcholinesterase expression resulted from events related to cell immortalization and did not result from activation by the large T antigen.
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Affiliation(s)
- M Kris
- Eppley Institute, University of Nebraska Medical Center, Omaha 68198
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