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Chow CFW, Ghosh S, Hadarovich A, Toth-Petroczy A. SHARK enables sensitive detection of evolutionary homologs and functional analogs in unalignable and disordered sequences. Proc Natl Acad Sci U S A 2024; 121:e2401622121. [PMID: 39383002 DOI: 10.1073/pnas.2401622121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 08/30/2024] [Indexed: 10/11/2024] Open
Abstract
Intrinsically disordered regions (IDRs) are structurally flexible protein segments with regulatory functions in multiple contexts, such as in the assembly of biomolecular condensates. Since IDRs undergo more rapid evolution than ordered regions, identifying homology of such poorly conserved regions remains challenging for state-of-the-art alignment-based methods that rely on position-specific conservation of residues. Thus, systematic functional annotation and evolutionary analysis of IDRs have been limited, despite them comprising ~21% of proteins. To accurately assess homology between unalignable sequences, we developed an alignment-free sequence comparison algorithm, SHARK (Similarity/Homology Assessment by Relating K-mers). We trained SHARK-dive, a machine learning homology classifier, which achieved superior performance to standard alignment-based approaches in assessing evolutionary homology in unalignable sequences. Furthermore, it correctly identified dissimilar but functionally analogous IDRs in IDR-replacement experiments reported in the literature, whereas alignment-based tools were incapable of detecting such functional relationships. SHARK-dive not only predicts functionally similar IDRs at a proteome-wide scale but also identifies cryptic sequence properties and motifs that drive remote homology and analogy, thereby providing interpretable and experimentally verifiable hypotheses of the sequence determinants that underlie such relationships. SHARK-dive acts as an alternative to alignment to facilitate systematic analysis and functional annotation of the unalignable protein universe.
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Affiliation(s)
- Chi Fung Willis Chow
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
- Center for Systems Biology Dresden, Dresden 01307, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden 01062, Germany
| | - Soumyadeep Ghosh
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
- Center for Systems Biology Dresden, Dresden 01307, Germany
| | - Anna Hadarovich
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
- Center for Systems Biology Dresden, Dresden 01307, Germany
| | - Agnes Toth-Petroczy
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
- Center for Systems Biology Dresden, Dresden 01307, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden 01062, Germany
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Tsai HC, Chang GRL, Tung MC, Tu MY, Chen IC, Liu YH, Cidem A, Chen CM. MicroRNA Signature in an In Vitro Keratinocyte Model of Diabetic Wound Healing. Int J Mol Sci 2024; 25:10125. [PMID: 39337611 PMCID: PMC11432929 DOI: 10.3390/ijms251810125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2024] [Revised: 09/12/2024] [Accepted: 09/18/2024] [Indexed: 09/30/2024] Open
Abstract
Treating diabetic wounds effectively remains a significant clinical challenge. Emerging studies suggest that microRNAs (miRNAs) play crucial roles in various physiological and pathological processes and hold promise as therapeutic tools. This study investigates the miRNA expression profile in keratinocytes using a cell model of diabetic wounds. Microarray analysis revealed that 43 miRNAs from wounded keratinocytes incubated under diabetic conditions (high glucose/hypoxia) exhibited a two-fold change in expression compared to those incubated under normal conditions (low glucose/normoxia). Quantitative RT-PCR confirmed significant differences in the expression of eight miRNAs, with miR-3138 and miR-3679-5p being further analyzed for their roles in keratinocyte migration. Transfection with a miR-3138 mimic and a miR-3679-5p inhibitor indicated that upregulation of miR-3138 and downregulation of miR-3679-5p enhance keratinocyte migration in both normal and diabetic wounds. Pathway and gene ontology (GO) analyses identified potential pathways and functional annotations associated with miR-3138 and miR-3679-5p in diabetic wound healing. Potential human gene targets of miR-3138 and miR-3679-5p were predicted using a three-way comparison of the TargetScan, miRDB, and DIANA databases. This study elucidates the miRNA expression signature of human keratinocytes in a diabetes-like environment, providing deeper insights into the pathogenesis of diabetic wounds.
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Affiliation(s)
- Hsin-Chung Tsai
- Department of Life Sciences, Doctorial Program in Translational Medicine, National Chung Hsing University, Taichung 402, Taiwan
- Department of Surgery, Taichung Hospital, Ministry of Health and Welfare, Taichung 403, Taiwan
| | - Gary Ro-Lin Chang
- Department of Life Sciences, Doctorial Program in Translational Medicine, National Chung Hsing University, Taichung 402, Taiwan
| | - Min-Che Tung
- Department of Surgery, Tungs' Taichung Metro Harbor Hospital, Taichung 435, Taiwan
| | - Min-Yu Tu
- Department of Life Sciences, Doctorial Program in Translational Medicine, National Chung Hsing University, Taichung 402, Taiwan
- Department of Orthopedic Surgery, Taichung Armed Forces General Hospital, Taichung 411, Taiwan
| | - I-Chien Chen
- Department of Life Sciences, Doctorial Program in Translational Medicine, National Chung Hsing University, Taichung 402, Taiwan
| | - Yu-Hsien Liu
- Department of Life Sciences, Doctorial Program in Translational Medicine, National Chung Hsing University, Taichung 402, Taiwan
- Department of Internal Medicine, Jen-Ai Hospital, Dali Branch, Taichung 402, Taiwan
| | - Abdulkadir Cidem
- Department of Life Sciences, Doctorial Program in Translational Medicine, National Chung Hsing University, Taichung 402, Taiwan
- Department of Molecular Biology and Genetics, Erzurum Technical University, Erzurum 25250, Turkey
| | - Chuan-Mu Chen
- Department of Life Sciences, Doctorial Program in Translational Medicine, National Chung Hsing University, Taichung 402, Taiwan
- The iEGG and Animal Biotechnology Research Center, National Chung Hsing University, Taichung 402, Taiwan
- Rong Hsing Research Center for Translational Medicine, Taichung Veterans General Hospital, Taichung 407, Taiwan
- Center for General Educational, National Quemoy University, Kinmen 892, Taiwan
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Palumbo S, Palumbo D, Cirillo G, Giurato G, Aiello F, Miraglia Del Giudice E, Grandone A. Methylome analysis in girls with idiopathic central precocious puberty. Clin Epigenetics 2024; 16:82. [PMID: 38909248 PMCID: PMC11193236 DOI: 10.1186/s13148-024-01683-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 05/22/2024] [Indexed: 06/24/2024] Open
Abstract
BACKGROUND Genetic and environmental factors are implicated in many developmental processes. Recent evidence, however, has suggested that epigenetic changes may also influence the onset of puberty or the susceptibility to a wide range of diseases later in life. The present study aims to investigate changes in genomic DNA methylation profiles associated with pubertal onset analyzing human peripheral blood leukocytes from three different groups of subjects: 19 girls with central precocious puberty (CPP), 14 healthy prepubertal girls matched by age and 13 healthy pubertal girls matched by pubertal stage. For this purpose, the comparisons were performed between pre- and pubertal controls to identify changes in normal pubertal transition and CPP versus pre- and pubertal controls. RESULTS Analysis of methylation changes associated with normal pubertal transition identified 1006 differentially methylated CpG sites, 86% of them were found to be hypermethylated in prepubertal controls. Some of these CpG sites reside in genes associated with the age of menarche or transcription factors involved in the process of pubertal development. Analysis of methylome profiles in CPP patients showed 65% and 55% hypomethylated CpG sites compared with prepubertal and pubertal controls, respectively. In addition, interestingly, our results revealed the presence of 43 differentially methylated genes coding for zinc finger (ZNF) proteins. Gene ontology and IPA analysis performed in the three groups studied revealed significant enrichment of them in some pathways related to neuronal communication (semaphorin and gustation pathways), estrogens action, some cancers (particularly breast and ovarian) or metabolism (particularly sirtuin). CONCLUSIONS The different methylation profiles of girls with normal and precocious puberty indicate that regulation of the pubertal process in humans is associated with specific epigenetic changes. Differentially methylated genes include ZNF genes that may play a role in developmental control. In addition, our data highlight changes in the methylation status of genes involved in signaling pathways that determine the migration and function of GnRH neurons and the onset of metabolic and neoplastic diseases that may be associated with CPP in later life.
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Affiliation(s)
- Stefania Palumbo
- Department of Women's and Children's Health and General and Specialized Surgery, University of Campania "Luigi Vanvitelli", Via Luigi De Crecchio 2, 80138, Naples, Italy.
| | - Domenico Palumbo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry SMS, University of Salerno, Salerno, Italy
| | - Grazia Cirillo
- Department of Women's and Children's Health and General and Specialized Surgery, University of Campania "Luigi Vanvitelli", Via Luigi De Crecchio 2, 80138, Naples, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry SMS, University of Salerno, Salerno, Italy
| | - Francesca Aiello
- Department of Women's and Children's Health and General and Specialized Surgery, University of Campania "Luigi Vanvitelli", Via Luigi De Crecchio 2, 80138, Naples, Italy
| | - Emanuele Miraglia Del Giudice
- Department of Women's and Children's Health and General and Specialized Surgery, University of Campania "Luigi Vanvitelli", Via Luigi De Crecchio 2, 80138, Naples, Italy
| | - Anna Grandone
- Department of Women's and Children's Health and General and Specialized Surgery, University of Campania "Luigi Vanvitelli", Via Luigi De Crecchio 2, 80138, Naples, Italy
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Du X, Yu L, Wang L, Yan X, Xu B, Chai F, Li D, Zi J, Zhang J, Jiang Y. Reduced Proliferative Capacity and Defense against Staphylococcus aureus in Human Nasal Mucosal Epithelium Lacking ZNF365. Int Arch Allergy Immunol 2024; 185:466-479. [PMID: 38354721 DOI: 10.1159/000536106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/22/2023] [Indexed: 02/16/2024] Open
Abstract
INTRODUCTION Chronic rhinosinusitis with nasal polyps (CRSwNP) is a common chronic inflammatory disease of the nose characterized by barrier disruption and environmental susceptibility, and the deletion of ZNF365 may be a factor inducing these manifestations. However, there is no study on the mechanism of action between CRSwNP and ZNF365. Therefore, this study focuses on the effect of the zinc finger protein ZNF365 on the proliferation of nasal mucosal epithelial cells and their defense against Staphylococcus aureus (S. aureus). METHODS Immunohistochemistry and Western blot were applied to verify the changes of ZNF365 expression in nasal polyp tissues and control tissues, as well as in primary epithelial cells. ZNF365 was knocked down in human nasal mucosa epithelial cell line (HNEpc), and the proliferation, migration, and transdifferentiation of epithelium were observed by immunofluorescence, QPCR, CCK8, and cell scratch assay. The changes of mesenchymal markers and TLR4-MAPK-NF-κB pathway were also observed after the addition of S. aureus. RESULTS ZNF365 expression was reduced in NP tissues and primary nasal mucosal epithelial cells compared to controls. Knockdown of ZNF365 in HNEpc resulted in decreased proliferation and migration ability of epithelial cells and abnormal epithelial differentiation (decreased expression of tight junction proteins). S. aureus stimulation further inhibited epithelial cell proliferation and migration, while elevated markers of epithelial-mesenchymal transition and inflammatory responses occurred. CONCLUSION ZNF365 is instrumental in maintaining the proliferative capacity of nasal mucosal epithelial cells and defending against the invasion of S. aureus. The findings suggest that ZNF365 may participate in the development of CRSwNP.
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Affiliation(s)
- Xiaoyun Du
- Department of Otolaryngology, Head and Neck Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China,
| | - Longgang Yu
- Department of Otolaryngology, Head and Neck Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Lin Wang
- Department of Otolaryngology, Head and Neck Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xudong Yan
- Department of Otolaryngology, Head and Neck Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Bingqing Xu
- Department of Otolaryngology, Head and Neck Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Fangyu Chai
- Department of Otolaryngology, Head and Neck Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Danyang Li
- Department of Otolaryngology, Head and Neck Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jiajia Zi
- Department of Otolaryngology, Head and Neck Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jisheng Zhang
- Department of Otolaryngology, Head and Neck Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yan Jiang
- Department of Otolaryngology, Head and Neck Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
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O’Sullivan J, Kothari C, Caron MC, Gagné JP, Jin Z, Nonfoux L, Beneyton A, Coulombe Y, Thomas M, Atalay N, Meng X, Milano L, Jean D, Boisvert FM, Kaufmann S, Hendzel M, Masson JY, Poirier G. ZNF432 stimulates PARylation and inhibits DNA resection to balance PARPi sensitivity and resistance. Nucleic Acids Res 2023; 51:11056-11079. [PMID: 37823600 PMCID: PMC10639050 DOI: 10.1093/nar/gkad791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 09/05/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023] Open
Abstract
Zinc finger (ZNF) motifs are some of the most frequently occurring domains in the human genome. It was only recently that ZNF proteins emerged as key regulators of genome integrity in mammalian cells. In this study, we report a new role for the Krüppel-type ZNF-containing protein ZNF432 as a novel poly(ADP-ribose) (PAR) reader that regulates the DNA damage response. We show that ZNF432 is recruited to DNA lesions via DNA- and PAR-dependent mechanisms. Remarkably, ZNF432 stimulates PARP-1 activity in vitro and in cellulo. Knockdown of ZNF432 inhibits phospho-DNA-PKcs and increases RAD51 foci formation following irradiation. Moreover, purified ZNF432 preferentially binds single-stranded DNA and impairs EXO1-mediated DNA resection. Consequently, the loss of ZNF432 in a cellular system leads to resistance to PARP inhibitors while its overexpression results in sensitivity. Taken together, our results support the emerging concept that ZNF-containing proteins can modulate PARylation, which can be embodied by the pivotal role of ZNF432 to finely balance the outcome of PARPi response by regulating homologous recombination.
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Affiliation(s)
- Julia O’Sullivan
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - Charu Kothari
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QCG1V 4G2, Canada
| | - Marie-Christine Caron
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - Jean-Philippe Gagné
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QCG1V 4G2, Canada
| | - Zhigang Jin
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, 11560 University Avenue, Edmonton, Alberta T6G 1Z2, Canada
| | - Louis Nonfoux
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QCG1V 4G2, Canada
| | - Adèle Beneyton
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - Yan Coulombe
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - Mélissa Thomas
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - Nurgul Atalay
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - X Wei Meng
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Larissa Milano
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - Dominique Jean
- Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - François-Michel Boisvert
- Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Scott H Kaufmann
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Michael J Hendzel
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, 11560 University Avenue, Edmonton, Alberta T6G 1Z2, Canada
| | - Jean-Yves Masson
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QCG1R 3S3, Canada
| | - Guy G Poirier
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QCG1V 4G2, Canada
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6
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Lack of ZNF365 Drives Senescence and Exacerbates Experimental Lung Fibrosis. Cells 2022; 11:cells11182848. [PMID: 36139424 PMCID: PMC9497065 DOI: 10.3390/cells11182848] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 11/17/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is characterized by aberrant activation of the alveolar epithelium, the expansion of the fibroblast population, and the accumulation of extracellular matrix. Global gene expression of human lung fibroblasts stimulated with TGFβ-1, a strong fibrotic mediator revealed the overexpression of ZNF365, a zinc finger protein implicated in cell cycle control and telomere stabilization. We evaluated the expression and localization of ZNF365 in IPF lungs and in the fibrotic response induced by bleomycin in WT and deficient mice of the orthologous gene Zfp365. In IPF, ZNF365 was overexpressed and localized in fibroblasts/myofibroblasts and alveolar epithelium. Bleomycin-induced lung fibrosis showed an upregulation of Zfp365 localized in lung epithelium and stromal cell populations. Zfp365 KO mice developed a significantly higher fibrotic response compared with WT mice by morphology and hydroxyproline content. Silencing ZNF365 in human lung fibroblasts and alveolar epithelial cells induced a significant reduction of growth rate and increased senescence markers, including Senescence Associated β Galactosidase activity, p53, p21, and the histone variant γH2AX. Our findings demonstrate that ZNF365 is upregulated in IPF and experimental lung fibrosis and suggest a protective role since its absence increases experimental lung fibrosis mechanistically associated with the induction of cell senescence.
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7
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Targeting SIRT2 Sensitizes Melanoma Cells to Cisplatin via an EGFR-Dependent Mechanism. Int J Mol Sci 2021; 22:ijms22095034. [PMID: 34068624 PMCID: PMC8126047 DOI: 10.3390/ijms22095034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/27/2021] [Accepted: 05/05/2021] [Indexed: 01/29/2023] Open
Abstract
Melanoma cells are resistant to most anticancer chemotherapeutics. Despite poor response rates and short-term efficacy, chemotherapy remains the main approach to treating this cancer. The underlying mechanisms of the intrinsic chemoresistance of melanoma remain unclear, but elucidating these mechanisms is important to improve the efficacy of chemotherapy regimens. Increasing evidence suggests that sirtuin 2 (SIRT2) plays a key role in the response of melanoma cells to chemotherapeutics; thus, in the present study, we evaluated the impact of shRNA-mediated and pharmacological inhibition of SIRT2 on the sensitivity of melanoma cells to cisplatin, which is used in several regimens to treat melanoma patients. We found that cells with SIRT2 inhibition revealed increased sensitivity to cisplatin and exhibited increased accumulation of γ-H2AX and reduced EGFR-AKT-RAF-ERK1/2 (epidermal growth factor receptor-protein B kinase-RAF kinase-extracellular signal-regulated kinase 1/2) pathway signaling compared to control cells. Thus, our results show that sirtuin 2 inhibition increased the in vitro efficacy of cisplatin against melanoma cells.
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Chasovskikh NY, Grechishnikova AY. Functional Annotation of Genes of Predisposition to Schizophrenia and Celiac Disease. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420100038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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p53 drives a transcriptional program that elicits a non-cell-autonomous response and alters cell state in vivo. Proc Natl Acad Sci U S A 2020; 117:23663-23673. [PMID: 32900967 DOI: 10.1073/pnas.2008474117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Cell stress and DNA damage activate the tumor suppressor p53, triggering transcriptional activation of a myriad of target genes. The molecular, morphological, and physiological consequences of this activation remain poorly understood in vivo. We activated a p53 transcriptional program in mice by deletion of Mdm2, a gene that encodes the major p53 inhibitor. By overlaying tissue-specific RNA-sequencing data from pancreas, small intestine, ovary, kidney, and heart with existing p53 chromatin immunoprecipitation (ChIP) sequencing, we identified a large repertoire of tissue-specific p53 genes and a common p53 transcriptional signature of seven genes, which included Mdm2 but not p21 Global p53 activation caused a metaplastic phenotype in the pancreas that was missing in mice with acinar-specific p53 activation, suggesting non-cell-autonomous effects. The p53 cellular response at single-cell resolution in the intestine altered transcriptional cell state, leading to a proximal enterocyte population enriched for genes within oxidative phosphorylation pathways. In addition, a population of active CD8+ T cells was recruited. Combined, this study provides a comprehensive profile of the p53 transcriptional response in vivo, revealing both tissue-specific transcriptomes and a unique signature, which were integrated to induce both cell-autonomous and non-cell-autonomous responses and transcriptional plasticity.
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Nguyen AP, Nicoletti P, Arnol D, Califano A, Rodríguez Martínez M. Identifying the Potential Mechanism of Action of SNPs Associated With Breast Cancer Susceptibility With GVITamIN. Front Bioeng Biotechnol 2020; 8:798. [PMID: 32850701 PMCID: PMC7417307 DOI: 10.3389/fbioe.2020.00798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 06/22/2020] [Indexed: 11/24/2022] Open
Abstract
In the last decade, a large number of genome-wide association studies have uncovered many single-nucleotide polymorphisms (SNPs) that are associated with complex traits and confer susceptibility to diseases, such as cancer. However, so far only a few heritable traits with medium-to-high penetrance have been identified. The vast majority of the discovered variants only leads to disease in combination with other still unknown factors. Furthermore, while many studies aimed to link the effect of SNPs to changes in molecular phenotypes, the analysis has been often focused on testing associations between a single SNP and a transcript, hence disregarding the dysregulation of gene regulatory networks that has been shown to play an essential role in disease onset, notably in cancer. Here we take a systems biology approach and develop GVITamIN (Genetic VarIaTIoN functional analysis tool), a new statistical and computational approach to characterize the effect of a SNP on both genes and transcriptional regulatory programs. GVITamIN exploits a novel statistical approach to combine the usually small effect of disease-susceptibility SNPs, and reveals important potential oncogenic mechanisms, hence taking one step further in the direction of understanding the SNP mechanism of action. We apply GVITamIN on a breast cancer cohort and identify well-known cancer-related transcription factors, such as CTCF, LEF1, and FOXA1, as TFs dysregulated by breast cancer-associated SNPs. Furthermore, our results reveal that SNPs located on the RAD51B gene are significantly associated with an abnormal regulatory activity, suggesting a pivotal role for homologous recombination repair mechanisms in breast cancer.
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Affiliation(s)
- An-Phi Nguyen
- IBM Research-Zurich, Zurich, Switzerland.,ETH-Zürich, Zurich, Switzerland
| | - Paola Nicoletti
- Herbert Irving Cancer Research Center, Columbia University Medical Center, New York, NY, United States
| | | | - Andrea Califano
- Herbert Irving Cancer Research Center, Columbia University Medical Center, New York, NY, United States.,Department of Systems Biology, Columbia University, New York, NY, United States.,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, United States.,Department of Biomedical Informatics, Columbia University, New York, NY, United States.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States.,Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States.,J.P. Sulzberger Columbia Genome Center, Columbia University, New York, NY, United States
| | - María Rodríguez Martínez
- Herbert Irving Cancer Research Center, Columbia University Medical Center, New York, NY, United States
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11
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Wang C, Liu S, Kuang Y, Hu X, Fang X. Downregulation of ZNF365 by methylation predicts poor prognosis in patients with colorectal cancer by decreasing phospho-p53 (Ser15) expression. Oncol Lett 2020; 20:85. [PMID: 32863918 PMCID: PMC7436887 DOI: 10.3892/ol.2020.11946] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 06/26/2020] [Indexed: 01/11/2023] Open
Abstract
ZNF365 is a transcription factor that plays important roles in different types of cancer, such as colorectal cancer, breast cancer and hepatocellular carcinoma. ZNF365 can promote stalled replication fork recovery to prevent genomic instability, which is a notable feature of sporadic and hereditary types of cancers. However, the function of ZNF365 in the tumor progression of colorectal cancer (CRC) remains unclear. Thus, immunohistochemical staining was used to investigate the association between ZNF365 expression and the clinicopathological characteristics of patients with colorectal cancer. The results demonstrated that ZNF365 protein was strongly expressed in the nucleus and cytoplasm of normal colorectal mucosa. Furthermore ZNF365, which is methylated and downregulated in most cancer cell lines and tissues, was significantly associated with lymph node metastasis (P=0.015), depth of invasion (P=0.031) and histopathological grading (P=0.042). A positive correlation was observed between ZNF365 expression and phosphorylated (P)-p53 (Ser15) protein expression (r=0.18; P=0.038). Survival analysis indicated that patients with high ZNF365 expression had a higher survival rate than those with low ZNF365 expression (P=0.009), suggesting that ZNF365 may be an independent prognostic factor for survival in colorectal cancer (P=0.046). Taken together, the results of the present study demonstrated that ZNF365 was frequently inactivated by promoter methylation and independently predicted poor prognosis in patients with colorectal cancer by downregulating P-p53 (Ser15) expression.
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Affiliation(s)
- Chan Wang
- Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang 310016, P.R. China
| | - Shuiping Liu
- Department of Cancer Pharmacology and Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, Holistic Integrative Pharmacy Institutes, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310012, P.R. China
| | - Yeye Kuang
- Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang 310016, P.R. China
| | - Xiaotong Hu
- Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang 310016, P.R. China.,Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang 310016, P.R. China
| | - Xiao Fang
- Department of Anesthesiology and Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang 310016, P.R. China
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Liu Y, Zhang Z, Li T, Li X, Zhang S, Li Y, Zhao W, Gu Y, Guo Z, Qi L. A Qualitative Transcriptional Signature for Predicting Recurrence Risk for High-Grade Serous Ovarian Cancer Patients Treated With Platinum-Taxane Adjuvant Chemotherapy. Front Oncol 2019; 9:1094. [PMID: 31681618 PMCID: PMC6813654 DOI: 10.3389/fonc.2019.01094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 10/04/2019] [Indexed: 11/13/2022] Open
Abstract
Resistance to platinum and taxane adjuvant chemotherapy (ACT) is the main cause of the recurrence and poor prognosis of high-grade serous ovarian cancer (HGS-OvCa) patients receiving platinum-taxane ACT after surgery. However, currently reported quantitative transcriptional signatures, which are commonly based on risk scores summarized from gene expression, are unsuitable for clinical application because of their high sensitivity to experimental batch effects and quality uncertainties of clinical samples. Using 226 samples of HGS-OvCa patients receiving platinum-taxane ACT in TCGA, we developed a qualitative transcriptional signature, consisting of four gene pairs whose within-samples relative expression orderings could robustly predict patient recurrence-free survival (RFS). In two independent test datasets, the predicted non-responders had significantly shorter RFS than the predicted responders (log-rank p < 0.05). In a test dataset containing data for patient pathological response state, the signature reclassified 12 out of 22 pathological complete response patients as non-responders and two out of 16 pathological non-complete response patients as responders. Notably, the 12 predicted non-responders in the pathological complete response group had significantly shorter RFS than the predicted responders (log-rank p = 0.0122). This qualitative transcriptional signature, which is insensitive to experimental batch effects and quality uncertainties of clinical samples, can individually identify HGS-OvCa patients who are more likely to benefit from platinum-taxane adjuvant chemotherapy.
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Affiliation(s)
- Yixin Liu
- Basic Medicine College, Harbin Medical University, Harbin, China
| | - Zheyang Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Tianhao Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xin Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Sainan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Ying Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Wenyuan Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yunyan Gu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zheng Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.,Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.,Key Laboratory of Medical Bioinformatics, Fuzhou, China
| | - Lishuang Qi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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13
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Du X, Zhou Y, Song L, Wang X, Zhang S. Zinc finger protein 365 is a new maternal LPS‐binding protein that defends zebrafish embryos against gram‐negative bacterial infections. FASEB J 2018; 32:979-994. [DOI: 10.1096/fj.201700694r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Affiliation(s)
- Xiaoyuan Du
- Department of Marine BiologyInstitute of Evolution and Marine BiodiversityOcean University of ChinaQingdaoChina
- Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Yang Zhou
- Department of Marine BiologyInstitute of Evolution and Marine BiodiversityOcean University of ChinaQingdaoChina
- Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Lili Song
- Department of Marine BiologyInstitute of Evolution and Marine BiodiversityOcean University of ChinaQingdaoChina
- Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Xia Wang
- Department of Marine BiologyInstitute of Evolution and Marine BiodiversityOcean University of ChinaQingdaoChina
- Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Shicui Zhang
- Department of Marine BiologyInstitute of Evolution and Marine BiodiversityOcean University of ChinaQingdaoChina
- Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
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14
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Chen G, Magis AT, Xu K, Park D, Yu DS, Owonikoko TK, Sica GL, Satola SW, Ramalingam SS, Curran WJ, Doetsch PW, Deng X. Targeting Mcl-1 enhances DNA replication stress sensitivity to cancer therapy. J Clin Invest 2017; 128:500-516. [PMID: 29227281 DOI: 10.1172/jci92742] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 11/02/2017] [Indexed: 12/21/2022] Open
Abstract
DNA double-strand breaks (DSBs) are mainly repaired either by homologous recombination (HR) or by nonhomologous end-joining (NHEJ) pathways. Here, we showed that myeloid cell leukemia sequence 1 (Mcl-1) acts as a functional switch in selecting between HR and NHEJ pathways. Mcl-1 was cell cycle-regulated during HR, with its expression peaking in S/G2 phase. While endogenous Mcl-1 depletion reduced HR and enhanced NHEJ, Mcl-1 overexpression resulted in a net increase in HR over NHEJ. Mcl-1 directly interacted with the dimeric Ku protein complex via its Bcl-2 homology 1 and 3 (BH1 and BH3) domains, which are required for Mcl-1 to inhibit Ku-mediated NHEJ. Mcl-1 also promoted DNA resection mediated by the Mre11 complex and HR-dependent DSB repair. Using the Mcl-1 BH1 domain as a docking site, we identified a small molecule, MI-223, that directly bound to BH1 and blocked Mcl-1-stimulated HR DNA repair, leading to sensitization of cancer cells to hydroxyurea- or olaparib-induced DNA replication stress. Combined treatment with MI-223 and hydroxyurea or olaparib exhibited a strong synergy against lung cancer in vivo. This mechanism-driven combination of agents provides a highly attractive therapeutic strategy to improve lung cancer outcomes.
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Affiliation(s)
- Guo Chen
- Department of Radiation Oncology, Emory University School of Medicine and Winship Cancer Institute of Emory University, Atlanta, Georgia, USA
| | | | - Ke Xu
- Department of Radiation Oncology, Emory University School of Medicine and Winship Cancer Institute of Emory University, Atlanta, Georgia, USA
| | - Dongkyoo Park
- Department of Radiation Oncology, Emory University School of Medicine and Winship Cancer Institute of Emory University, Atlanta, Georgia, USA
| | - David S Yu
- Department of Radiation Oncology, Emory University School of Medicine and Winship Cancer Institute of Emory University, Atlanta, Georgia, USA
| | | | | | | | | | - Walter J Curran
- Department of Radiation Oncology, Emory University School of Medicine and Winship Cancer Institute of Emory University, Atlanta, Georgia, USA
| | - Paul W Doetsch
- Department of Radiation Oncology, Emory University School of Medicine and Winship Cancer Institute of Emory University, Atlanta, Georgia, USA.,Department of Biochemistry, Emory University School of Medicine and Winship Cancer Institute of Emory University, Atlanta, Georgia, USA
| | - Xingming Deng
- Department of Radiation Oncology, Emory University School of Medicine and Winship Cancer Institute of Emory University, Atlanta, Georgia, USA
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15
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Lew D, Yoon SM, Yan X, Robbins L, Haritunians T, Liu Z, Li D, McGovern DPB. Genetic associations with adverse events from anti-tumor necrosis factor therapy in inflammatory bowel disease patients. World J Gastroenterol 2017; 23:7265-7273. [PMID: 29142473 PMCID: PMC5677193 DOI: 10.3748/wjg.v23.i40.7265] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 08/25/2017] [Accepted: 09/13/2017] [Indexed: 02/06/2023] Open
Abstract
AIM To study the type and frequency of adverse events associated with anti-tumor necrosis factor (TNF) therapy and evaluate for any serologic and genetic associations.
METHODS This study was a retrospective review of patients attending the inflammatory bowel disease (IBD) centers at Cedars-Sinai IBD Center from 2005-2016. Adverse events were identified via chart review. IBD serologies were measured by ELISA. DNA samples were genotyped at Cedars-Sinai using Illumina Infinium Immunochipv1 array per manufacturer’s protocol. SNPs underwent methodological review and were evaluated using several SNP statistic parameters to ensure optimal allele-calling. Standard and rigorous QC criteria were applied to the genetic data, which was generated using immunochip. Genetic association was assessed by logistic regression after correcting for population structure.
RESULTS Altogether we identified 1258 IBD subjects exposed to anti-TNF agents in whom Immunochip data were available. 269/1258 patients (21%) were found to have adverse events to an anti-TNF-α agent that required the therapy to be discontinued. 25% of women compared to 17% of men experienced an adverse event. All adverse events resolved after discontinuing the anti-TNF agent. In total: n = 66 (5%) infusion reactions; n = 49 (4%) allergic/serum sickness reactions; n = 19 (1.5%) lupus-like reactions, n = 52 (4%) rash, n = 18 (1.4%) infections. In Crohn’s disease, IgA ASCA (P = 0.04) and IgG-ASCA (P = 0.02) levels were also lower in patients with any adverse events, and anti-I2 level in ulcerative colitis was significantly associated with infusion reactions (P = 0.008). The logistic regression/human annotation and network analyses performed on the Immunochip data implicated the following five signaling pathways: JAK-STAT (Janus Kinase-signal transducer and activator of transcription), measles, IBD, cytokine-cytokine receptor interaction, and toxoplasmosis for any adverse event.
CONCLUSION Our study shows 1 in 5 IBD patients experience an adverse event to anti-TNF therapy with novel serologic, genetic , and pathways associations.
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Affiliation(s)
- Daniel Lew
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Soon Man Yoon
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Xiaofei Yan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Lori Robbins
- Department of Gastroenterology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Zhenqiu Liu
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Dalin Li
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Dermot PB McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
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16
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El Husseini N, Schlisser AE, Hales BF. Editor's Highlight: Hydroxyurea Exposure Activates the P53 Signaling Pathway in Murine Organogenesis-Stage Embryos. Toxicol Sci 2016; 152:297-308. [PMID: 27208086 DOI: 10.1093/toxsci/kfw089] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Hydroxyurea, an anticancer agent and potent teratogen, induces oxidative stress and activates a DNA damage response pathway in the gestation day (GD) 9 mouse embryo. To delineate the stress response pathways activated by this drug, we investigated the effect of hydroxyurea exposure on the transcriptome of GD 9 embryos. Timed pregnant CD-1 mice were treated with saline or hydroxyurea (400 mg/kg or 600 mg/kg) on GD 9; embryonic gene and protein expression were examined 3 h later. Microarray analysis revealed that the expression of 1346 probe sets changed significantly in embryos exposed to hydroxyurea compared with controls; the P53 signaling pathway was highly affected. In addition, P53 related family members, P63 and P73, were predicted to be activated and had common and unique downstream targets. Western blot analysis revealed that active phospho-P53 was significantly increased in drug-exposed embryos; confocal microscopy showed that the translocation of phospho-P53 to the nucleus was widespread in the embryo. Furthermore, qRT-PCR showed that the expression of P53-regulated genes (Cdkn1A, Fas, and Trp53inp1) was significantly upregulated in hydroxyurea-exposed embryos; the concentration of the redox sensitive P53INP1 protein was also increased in a hydroxyurea dose-dependent fashion. Thus, hydroxyurea elicits a significant effect on the transcriptome of the organogenesis stage murine embryo, activating several key developmental signaling pathways related to DNA damage and oxidative stress. We propose that the P53 pathway plays a central role in the embryonic stress response and the developmental outcome after teratogen exposure.
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Affiliation(s)
- Nazem El Husseini
- *Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, H3G 1Y6, Canada
| | - Ava E Schlisser
- *Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, H3G 1Y6, Canada
| | - Barbara F Hales
- *Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, H3G 1Y6, Canada
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17
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Darabi H, McCue K, Beesley J, Michailidou K, Nord S, Kar S, Humphreys K, Thompson D, Ghoussaini M, Bolla MK, Dennis J, Wang Q, Canisius S, Scott CG, Apicella C, Hopper JL, Southey MC, Stone J, Broeks A, Schmidt MK, Scott RJ, Lophatananon A, Muir K, Beckmann MW, Ekici AB, Fasching PA, Heusinger K, Dos-Santos-Silva I, Peto J, Tomlinson I, Sawyer EJ, Burwinkel B, Marme F, Guénel P, Truong T, Bojesen SE, Flyger H, Benitez J, González-Neira A, Anton-Culver H, Neuhausen SL, Arndt V, Brenner H, Engel C, Meindl A, Schmutzler RK, Arnold N, Brauch H, Hamann U, Chang-Claude J, Khan S, Nevanlinna H, Ito H, Matsuo K, Bogdanova NV, Dörk T, Lindblom A, Margolin S, Kosma VM, Mannermaa A, Tseng CC, Wu AH, Floris G, Lambrechts D, Rudolph A, Peterlongo P, Radice P, Couch FJ, Vachon C, Giles GG, McLean C, Milne RL, Dugué PA, Haiman CA, Maskarinec G, Woolcott C, Henderson BE, Goldberg MS, Simard J, Teo SH, Mariapun S, Helland Å, Haakensen V, Zheng W, Beeghly-Fadiel A, Tamimi R, Jukkola-Vuorinen A, Winqvist R, Andrulis IL, Knight JA, Devilee P, Tollenaar RAEM, Figueroa J, García-Closas M, Czene K, Hooning MJ, Tilanus-Linthorst M, Li J, Gao YT, Shu XO, Cox A, Cross SS, Luben R, Khaw KT, Choi JY, Kang D, Hartman M, Lim WY, Kabisch M, Torres D, Jakubowska A, Lubinski J, McKay J, Sangrajrang S, Toland AE, Yannoukakos D, Shen CY, Yu JC, Ziogas A, Schoemaker MJ, Swerdlow A, Borresen-Dale AL, Kristensen V, French JD, Edwards SL, Dunning AM, Easton DF, Hall P, Chenevix-Trench G. Polymorphisms in a Putative Enhancer at the 10q21.2 Breast Cancer Risk Locus Regulate NRBF2 Expression. Am J Hum Genet 2015; 97:22-34. [PMID: 26073781 PMCID: PMC4572510 DOI: 10.1016/j.ajhg.2015.05.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 05/01/2015] [Indexed: 12/13/2022] Open
Abstract
Genome-wide association studies have identified SNPs near ZNF365 at 10q21.2 that are associated with both breast cancer risk and mammographic density. To identify the most likely causal SNPs, we fine mapped the association signal by genotyping 428 SNPs across the region in 89,050 European and 12,893 Asian case and control subjects from the Breast Cancer Association Consortium. We identified four independent sets of correlated, highly trait-associated variants (iCHAVs), three of which were located within ZNF365. The most strongly risk-associated SNP, rs10995201 in iCHAV1, showed clear evidence of association with both estrogen receptor (ER)-positive (OR = 0.85 [0.82-0.88]) and ER-negative (OR = 0.87 [0.82-0.91]) disease, and was also the SNP most strongly associated with percent mammographic density. iCHAV2 (lead SNP, chr10: 64,258,684:D) and iCHAV3 (lead SNP, rs7922449) were also associated with ER-positive (OR = 0.93 [0.91-0.95] and OR = 1.06 [1.03-1.09]) and ER-negative (OR = 0.95 [0.91-0.98] and OR = 1.08 [1.04-1.13]) disease. There was weaker evidence for iCHAV4, located 5' of ADO, associated only with ER-positive breast cancer (OR = 0.93 [0.90-0.96]). We found 12, 17, 18, and 2 candidate causal SNPs for breast cancer in iCHAVs 1-4, respectively. Chromosome conformation capture analysis showed that iCHAV2 interacts with the ZNF365 and NRBF2 (more than 600 kb away) promoters in normal and cancerous breast epithelial cells. Luciferase assays did not identify SNPs that affect transactivation of ZNF365, but identified a protective haplotype in iCHAV2, associated with silencing of the NRBF2 promoter, implicating this gene in the etiology of breast cancer.
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Affiliation(s)
- Hatef Darabi
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Karen McCue
- Department of Genetics, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Jonathan Beesley
- Department of Genetics, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Silje Nord
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, 0310 Oslo, Norway; K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Kirkeveien 166, 0450 Oslo, Norway
| | - Siddhartha Kar
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Keith Humphreys
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Deborah Thompson
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Maya Ghoussaini
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Sander Canisius
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands
| | - Christopher G Scott
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Carmel Apicella
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Melissa C Southey
- Department of Pathology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Jennifer Stone
- Centre for Genetic Origins of Health and Disease, University of Western Australia, Crawley, WA 6009, Australia
| | - Annegien Broeks
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands
| | - Marjanka K Schmidt
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands
| | - Rodney J Scott
- Discipline of Medical Genetics, School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, Newcastle, NSW 2308, Australia; Division of Molecular Medicine, Pathology North, John Hunter Hospital and The Hunter Medical Research Institute, Newcastle, NSW 2305, Australia
| | - Artitaya Lophatananon
- Division of Health Sciences, Warwick Medical School, Warwick University, Coventry CV4 7AL, UK
| | - Kenneth Muir
- Division of Health Sciences, Warwick Medical School, Warwick University, Coventry CV4 7AL, UK; Institute of Population Health, University of Manchester, Manchester M13 9PL, UK
| | - Matthias W Beckmann
- University Breast Center Franconia, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany
| | - Peter A Fasching
- University Breast Center Franconia, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany; Department of Medicine Division of Hematology and Oncology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Katharina Heusinger
- University Breast Center Franconia, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany
| | - Isabel Dos-Santos-Silva
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics and Oxford Biomedical Research Centre, University of Oxford, Oxford OX3 7BN, UK
| | - Elinor J Sawyer
- Research Oncology, Division of Cancer Studies, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Barbara Burwinkel
- National Center for Tumor Diseases, University of Heidelberg, 69120 Heidelberg, Germany; Division of Molecular Genetic Epidemiology, German Cancer Research Centre (DZFK), 69047 Heidelberg, Germany
| | - Frederik Marme
- National Center for Tumor Diseases, University of Heidelberg, 69120 Heidelberg, Germany; Department of Obstetrics and Gynecology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Pascal Guénel
- University Paris-Sud, UMRS 1018, 94807 Villejuif, France; INSERM (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer, 94807 Villejuif, France
| | - Thérèse Truong
- University Paris-Sud, UMRS 1018, 94807 Villejuif, France; INSERM (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer, 94807 Villejuif, France
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, 2730 Herlev, Denmark; Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, 2730 Herlev, Denmark; Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Henrik Flyger
- Department of Breast Surgery, Herlev Hospital, Copenhagen University Hospital, 2730 Herlev, Denmark
| | - Javier Benitez
- Human Genotyping (CEGEN) Unit, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain; Human Genetics Group, Spanish National Cancer Centre (CNIO), Madrid 28029, Spain; Biomedical Network on Rare Diseases (CIBERER), Madrid 28029, Spain
| | - Anna González-Neira
- Human Genotyping (CEGEN) Unit, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Hoda Anton-Culver
- Department of Epidemiology, University of California Irvine, Irvine, CA 92697, USA
| | | | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Division of Preventive Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, 04107 Leipzig, Germany
| | - Alfons Meindl
- Division of Gynaecology and Obstetrics, Technische Universität München, 81675 Munich, Germany
| | - Rita K Schmutzler
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne 50932, Germany; Center for Hereditary Breast and Ovarian Cancer, Medical Faculty, University Hospital Cologne, Cologne 50937, Germany; Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne 50937, Germany
| | - Norbert Arnold
- Department of Gynaecology and Obstetrics, University Hospital of Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, 24105 Kiel, Germany
| | - Hiltrud Brauch
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; University of Tübingen, 72074 Tübingen, Germany
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Sofia Khan
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, 00029 HUS, Finland
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, 00029 HUS, Finland
| | - Hidemi Ito
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Aichi 464-8681, Japan
| | - Keitaro Matsuo
- Department of Preventive Medicine, Kyushu University Faculty of Medical Sciences, Fukuoka 812-8582, Japan
| | - Natalia V Bogdanova
- Department of Radiation Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, 30625 Hannover, Germany
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm 17177, Sweden
| | - Sara Margolin
- Department of Oncology - Pathology, Karolinska Institutet, Stockholm 17177, Sweden
| | - Veli-Matti Kosma
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio 70211, Finland; Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio 70211, Finland; Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio 70211, Finland
| | - Arto Mannermaa
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio 70211, Finland; Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio 70211, Finland; Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio 70211, Finland
| | - Chiu-Chen Tseng
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | | | - Diether Lambrechts
- Vesalius Research Center (VRC), VIB, Leuven 3000, Belgium; Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven 3000, Belgium
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Paolo Peterlongo
- IFOM, the FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology, 20139 Milan, Italy
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT), 20133 Milan, Italy
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Celine Vachon
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3010, Australia; Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC 3053, Australia
| | - Catriona McLean
- Anatomical Pathology, The Alfred Hospital, Melbourne, VIC 3004, Australia
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3010, Australia; Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC 3053, Australia
| | - Pierre-Antoine Dugué
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC 3053, Australia
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Gertraud Maskarinec
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Christy Woolcott
- Departments of Obstetrics & Gynaecology and Pediatrics, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Mark S Goldberg
- Department of Medicine, McGill University, Montreal, QC H3A 1W7, Canada; Division of Clinical Epidemiology, McGill University Health Centre, Royal Victoria Hospital, Montreal, QC H3H 2R9, Canada
| | - Jacques Simard
- Centre Hospitalier Universitaire de Québec Research Center and Laval University, Quebec City, QC G1V 4G2, Canada
| | - Soo H Teo
- Breast Cancer Research Unit, University Malaya Cancer Research Institute, University Malaya Medical Centre (UMMC), 50603 Kuala Lumpur, Malaysia; Cancer Research Initiatives Foundation, Sime Darby Medical Centre, 47500 Subang Jaya, Malaysia
| | - Shivaani Mariapun
- Breast Cancer Research Unit, University Malaya Cancer Research Institute, University Malaya Medical Centre (UMMC), 50603 Kuala Lumpur, Malaysia; Cancer Research Initiatives Foundation, Sime Darby Medical Centre, 47500 Subang Jaya, Malaysia
| | - Åslaug Helland
- Department of Oncology, Oslo University Hospital, Radiumhospitalet, 0310 Oslo, Norway
| | - Vilde Haakensen
- Department of Genetics, Oslo University Hospital, Radiumhospitalet, 0310 Oslo, Norway
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Alicia Beeghly-Fadiel
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Rulla Tamimi
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA; Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - Arja Jukkola-Vuorinen
- Department of Oncology, Oulu University Hospital and University of Oulu, 90014 Oulu, Finland
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Chemistry and Biocenter Oulu, University of Oulu, 90014 Oulu, Finland; Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre NordLab, 90220 Oulu, Finland
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Departments of Molecular Genetics and Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 3G3, Canada
| | - Julia A Knight
- Prosserman Centre for Health Research, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5S 3G3, Canada
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Robert A E M Tollenaar
- Department of Surgical Oncology, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands
| | - Jonine Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD 20850, USA
| | - Montserrat García-Closas
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton SM2 5NG, UK; Division of Cancer Studies, Breakthrough Breast Cancer Research Centre, London SW3 6JB, UK
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Maartje J Hooning
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3008 AE Rotterdam, the Netherlands
| | | | - Jingmei Li
- Human Genetics Division, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Xuhui, Shanghai 200031, China
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Angela Cox
- Sheffield Cancer Research Centre, Department of Oncology, University of Sheffield, Sheffield S10 2RX, UK
| | - Simon S Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
| | - Robert Luben
- Clinical Gerontology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Kay-Tee Khaw
- Department of Public Health and Primary Care, University of Cambridge, Cambridge CB2 1TN, UK
| | - Ji-Yeob Choi
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul 110-799, Korea; Department of Surgery, Seoul National University College of Medicine, Seoul 110-799, Korea
| | - Daehee Kang
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul 110-799, Korea; Department of Surgery, Seoul National University College of Medicine, Seoul 110-799, Korea; Department of Preventive Medicine, Seoul National University College of Medicine, Seoul 110-799, Korea
| | - Mikael Hartman
- Saw Swee Hock School of Public Health, National University of Singapore and Department of Surgery, National University Health System, Singapore 117597, Singapore
| | - Wei Yen Lim
- Saw Swee Hock School of Public Health, National University of Singapore and Department of Surgery, National University Health System, Singapore 117597, Singapore; Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore 119228, Singapore
| | - Maria Kabisch
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota 12362, Columbia
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, 70-115 Szczecin, Poland
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, 70-115 Szczecin, Poland
| | - James McKay
- International Agency for Research on Cancer, 69372 Lyon, CEDEX 08, France
| | | | - Amanda E Toland
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, IRRP, National Centre for Scientific Research "Demokritos," Aghia Paraskevi Attikis, 153 10 Athens, Greece
| | - Chen-Yang Shen
- Taiwan Biobank, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan; School of Public Health, China Medical University, Taichung 40402, Taiwan
| | - Jyh-Cherng Yu
- Department of Surgery, Tri-Service General Hospital, Taipei 114, Taiwan
| | - Argyrios Ziogas
- Department of Epidemiology, University of California Irvine, Irvine, CA 92697, USA
| | - Minouk J Schoemaker
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton SM2 5NG, UK
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton SM2 5NG, UK; Division of Breast Cancer Research, Institute of Cancer Research, Sutton SM2 5NG, UK
| | - Anne-Lise Borresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, 0310 Oslo, Norway; Institute of Clinical Medicine, University of Oslo (UiO), Oslo 0316, Norway
| | - Vessela Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, 0310 Oslo, Norway; Institute of Clinical Medicine, University of Oslo (UiO), Oslo 0316, Norway; Department of Clinical Molecular Biology (EpiGen), University of Oslo (UiO), Oslo 0316, Norway
| | - Juliet D French
- Department of Genetics, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Stacey L Edwards
- Department of Genetics, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Georgia Chenevix-Trench
- Department of Genetics, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.
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18
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Pino-Yanes M, Gignoux CR, Galanter JM, Levin AM, Campbell CD, Eng C, Huntsman S, Nishimura KK, Gourraud PA, Mohajeri K, O'Roak BJ, Hu D, Mathias RA, Nguyen EA, Roth LA, Padhukasahasram B, Moreno-Estrada A, Sandoval K, Winkler CA, Lurmann F, Davis A, Farber HJ, Meade K, Avila PC, Serebrisky D, Chapela R, Ford JG, Lenoir MA, Thyne SM, Brigino-Buenaventura E, Borrell LN, Rodriguez-Cintron W, Sen S, Kumar R, Rodriguez-Santana JR, Bustamante CD, Martinez FD, Raby BA, Weiss ST, Nicolae DL, Ober C, Meyers DA, Bleecker ER, Mack SJ, Hernandez RD, Eichler EE, Barnes KC, Williams LK, Torgerson DG, Burchard EG. Genome-wide association study and admixture mapping reveal new loci associated with total IgE levels in Latinos. J Allergy Clin Immunol 2015; 135:1502-10. [PMID: 25488688 PMCID: PMC4458233 DOI: 10.1016/j.jaci.2014.10.033] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 09/06/2014] [Accepted: 10/15/2014] [Indexed: 12/20/2022]
Abstract
BACKGROUND IgE is a key mediator of allergic inflammation, and its levels are frequently increased in patients with allergic disorders. OBJECTIVE We sought to identify genetic variants associated with IgE levels in Latinos. METHODS We performed a genome-wide association study and admixture mapping of total IgE levels in 3334 Latinos from the Genes-environments & Admixture in Latino Americans (GALA II) study. Replication was evaluated in 454 Latinos, 1564 European Americans, and 3187 African Americans from independent studies. RESULTS We confirmed associations of 6 genes identified by means of previous genome-wide association studies and identified a novel genome-wide significant association of a polymorphism in the zinc finger protein 365 gene (ZNF365) with total IgE levels (rs200076616, P = 2.3 × 10(-8)). We next identified 4 admixture mapping peaks (6p21.32-p22.1, 13p22-31, 14q23.2, and 22q13.1) at which local African, European, and/or Native American ancestry was significantly associated with IgE levels. The most significant peak was 6p21.32-p22.1, where Native American ancestry was associated with lower IgE levels (P = 4.95 × 10(-8)). All but 22q13.1 were replicated in an independent sample of Latinos, and 2 of the peaks were replicated in African Americans (6p21.32-p22.1 and 14q23.2). Fine mapping of 6p21.32-p22.1 identified 6 genome-wide significant single nucleotide polymorphisms in Latinos, 2 of which replicated in European Americans. Another single nucleotide polymorphism was peak-wide significant within 14q23.2 in African Americans (rs1741099, P = 3.7 × 10(-6)) and replicated in non-African American samples (P = .011). CONCLUSION We confirmed genetic associations at 6 genes and identified novel associations within ZNF365, HLA-DQA1, and 14q23.2. Our results highlight the importance of studying diverse multiethnic populations to uncover novel loci associated with total IgE levels.
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Affiliation(s)
- Maria Pino-Yanes
- Department of Medicine, University of California, San Francisco, Calif; CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
| | - Christopher R Gignoux
- Department of Medicine, University of California, San Francisco, Calif; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, Calif; Department of Genetics, Stanford University, Palo Alto, Calif
| | - Joshua M Galanter
- Department of Medicine, University of California, San Francisco, Calif; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, Calif
| | - Albert M Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Mich
| | | | - Celeste Eng
- Department of Medicine, University of California, San Francisco, Calif
| | - Scott Huntsman
- Department of Medicine, University of California, San Francisco, Calif
| | | | | | - Kiana Mohajeri
- Department of Genome Sciences, University of Washington, Seattle, Wash
| | - Brian J O'Roak
- Department of Genome Sciences, University of Washington, Seattle, Wash; Molecular & Medical Genetics Department, Oregon Health and Science University, Portland, Ore
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco, Calif
| | - Rasika A Mathias
- Division of Allergy & Clinical Immunology, Department of Medicine, Johns Hopkins University, Baltimore, Md
| | | | - Lindsey A Roth
- Department of Medicine, University of California, San Francisco, Calif
| | - Badri Padhukasahasram
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, Mich
| | | | - Karla Sandoval
- Department of Genetics, Stanford University, Palo Alto, Calif
| | - Cheryl A Winkler
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Leidos Biomedical, Frederick National Laboratory for Cancer Research, Frederick, Md
| | | | - Adam Davis
- Children's Hospital and Research Center Oakland, Oakland, Calif
| | - Harold J Farber
- Department of Pediatrics, Section of Pulmonology, Baylor College of Medicine and Texas Children's Hospital, Houston, Tex
| | - Kelley Meade
- Children's Hospital and Research Center Oakland, Oakland, Calif
| | - Pedro C Avila
- Department of Medicine, Northwestern University, Chicago, Ill
| | | | - Rocio Chapela
- Instituto Nacional de Enfermedades Respiratorias (INER), Mexico City, Mexico
| | - Jean G Ford
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Md
| | | | - Shannon M Thyne
- Department of Pediatrics, University of California San Francisco, San Francisco General Hospital, San Francisco, Calif
| | | | - Luisa N Borrell
- Department of Health Sciences, Graduate Program in Public Health, City University of New York, Bronx, NY
| | | | - Saunak Sen
- Department of Epidemiology and Biostatistics, University of California, San Francisco, Calif
| | - Rajesh Kumar
- Children's Memorial Hospital and the Feinberg School of Medicine, Northwestern University, Chicago, Ill
| | | | | | - Fernando D Martinez
- Arizona Respiratory Center, University of Arizona, Tucson, Ariz; BIO5 Institute, University of Arizona, Tucson, Ariz
| | - Benjamin A Raby
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Dan L Nicolae
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | - Deborah A Meyers
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC
| | - Eugene R Bleecker
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC
| | - Steven J Mack
- Children's Hospital Oakland Research Institute, Oakland, Calif
| | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, Calif
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington, Seattle, Wash; Howard Hughes Medical Institute, Seattle, Wash
| | - Kathleen C Barnes
- Division of Allergy & Clinical Immunology, Department of Medicine, Johns Hopkins University, Baltimore, Md
| | - L Keoki Williams
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, Mich; Department of Internal Medicine, Henry Ford Health System, Detroit, Mich
| | - Dara G Torgerson
- Department of Medicine, University of California, San Francisco, Calif
| | - Esteban G Burchard
- Department of Medicine, University of California, San Francisco, Calif; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, Calif
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19
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Chaste P, Klei L, Sanders SJ, Hus V, Murtha MT, Lowe JK, Willsey AJ, Moreno-De-Luca D, Yu TW, Fombonne E, Geschwind D, Grice DE, Ledbetter DH, Mane SM, Martin DM, Morrow EM, Walsh CA, Sutcliffe JS, Lese Martin C, Beaudet AL, Lord C, State MW, Cook EH, Devlin B. A genome-wide association study of autism using the Simons Simplex Collection: Does reducing phenotypic heterogeneity in autism increase genetic homogeneity? Biol Psychiatry 2015; 77:775-84. [PMID: 25534755 PMCID: PMC4379124 DOI: 10.1016/j.biopsych.2014.09.017] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Revised: 09/02/2014] [Accepted: 09/03/2014] [Indexed: 12/13/2022]
Abstract
BACKGROUND Phenotypic heterogeneity in autism has long been conjectured to be a major hindrance to the discovery of genetic risk factors, leading to numerous attempts to stratify children based on phenotype to increase power of discovery studies. This approach, however, is based on the hypothesis that phenotypic heterogeneity closely maps to genetic variation, which has not been tested. Our study examines the impact of subphenotyping of a well-characterized autism spectrum disorder (ASD) sample on genetic homogeneity and the ability to discover common genetic variants conferring liability to ASD. METHODS Genome-wide genotypic data of 2576 families from the Simons Simplex Collection were analyzed in the overall sample and phenotypic subgroups defined on the basis of diagnosis, IQ, and symptom profiles. We conducted a family-based association study, as well as estimating heritability and evaluating allele scores for each phenotypic subgroup. RESULTS Association analyses revealed no genome-wide significant association signal. Subphenotyping did not increase power substantially. Moreover, allele scores built from the most associated single nucleotide polymorphisms, based on the odds ratio in the full sample, predicted case status in subsets of the sample equally well and heritability estimates were very similar for all subgroups. CONCLUSIONS In genome-wide association analysis of the Simons Simplex Collection sample, reducing phenotypic heterogeneity had at most a modest impact on genetic homogeneity. Our results are based on a relatively small sample, one with greater homogeneity than the entire population; if they apply more broadly, they imply that analysis of subphenotypes is not a productive path forward for discovering genetic risk variants in ASD.
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Affiliation(s)
- Pauline Chaste
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; FondaMental Foundation, Créteil; Centre Hospitalier Sainte Anne, Paris, France.
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Stephan J Sanders
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut; Department of Psychiatry, University of California at San Francisco, San Francisco, California
| | - Vanessa Hus
- Department of Psychology, University of Michigan, Ann Arbor, Michigan
| | - Michael T Murtha
- Program on Neurogenetics, Yale University School of Medicine, New Haven, Connecticut
| | - Jennifer K Lowe
- Neurogenetics Program, Department of Neurology and Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - A Jeremy Willsey
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut; Department of Psychiatry, University of California at San Francisco, San Francisco, California
| | - Daniel Moreno-De-Luca
- Program on Neurogenetics, Yale University School of Medicine, New Haven, Connecticut; Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut
| | - Timothy W Yu
- Division of Genetics, Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts
| | - Eric Fombonne
- Department of Psychiatry and Institute for Development and Disability, Oregon Health & Science University, Portland, Oregon
| | - Daniel Geschwind
- Neurogenetics Program, Department of Neurology and Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Dorothy E Grice
- Department of Psychiatry, Mount Sinai School of Medicine, New York, New York
| | - David H Ledbetter
- Autism and Developmental Medicine Institute, Geisinger Health System, Danville, Pennsylvania
| | | | - Donna M Martin
- Departments of Pediatrics and Human Genetics, University of Michigan Medical Center, Ann Arbor, Michigan
| | - Eric M Morrow
- Department of Molecular Biology, Cell Biology and Biochemistry, and Department of Psychiatry and Human Behavior, Brown University, Providence, Rhode Island
| | - Christopher A Walsh
- Howard Hughes Medical Institute and Division of Genetics, Children's Hospital Boston, and Neurology and Pediatrics, Harvard Medical School Center for Life Sciences, Boston, Massachusetts
| | - James S Sutcliffe
- Departments of Molecular Physiology & Biophysics and Psychiatry, Vanderbilt Brain Institute, Vanderbilt University, Nashville, Tennessee
| | - Christa Lese Martin
- Autism and Developmental Medicine Institute, Geisinger Health System, Danville, Pennsylvania
| | - Arthur L Beaudet
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Catherine Lord
- Center for Autism and the Developing Brain, Weill Cornell Medical College, White Plains, New York
| | - Matthew W State
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut; Department of Psychiatry, University of California at San Francisco, San Francisco, California
| | - Edwin H Cook
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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