1
|
Durand A, Winkler CA, Vince N, Douillard V, Geffard E, Binns-Roemer E, Ng DK, Gourraud PA, Reidy K, Warady B, Furth S, Kopp JB, Kaskel FJ, Limou S. Identification of Novel Genetic Risk Factors for Focal Segmental Glomerulosclerosis in Children: Results From the Chronic Kidney Disease in Children (CKiD) Cohort. Am J Kidney Dis 2023; 81:635-646.e1. [PMID: 36623684 DOI: 10.1053/j.ajkd.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 11/02/2022] [Indexed: 01/09/2023]
Abstract
RATIONALE & OBJECTIVE Focal segmental glomerulosclerosis (FSGS) is a major cause of pediatric nephrotic syndrome, and African Americans exhibit an increased risk for developing FSGS compared with other populations. Predisposing genetic factors have previously been described in adults. Here we performed genomic screening of primary FSGS in a pediatric African American population. STUDY DESIGN Prospective cohort with case-control genetic association study design. SETTING & PARTICIPANTS 140 African American children with chronic kidney disease from the Chronic Kidney Disease in Children (CKiD) cohort, including 32 cases with FSGS. PREDICTORS Over 680,000 common single-nucleotide polymorphisms (SNPs) were tested for association. We also ran a pathway enrichment analysis and a human leucocyte antigen (HLA)-focused association study. OUTCOME Primary biopsy-proven pediatric FSGS. ANALYTICAL APPROACH Multivariate logistic regression models. RESULTS The genome-wide association study revealed 169 SNPs from 14 independent loci significantly associated with FSGS (false discovery rate [FDR]<5%). We observed notable signals for genetic variants within the APOL1 (P=8.6×10-7; OR, 25.8 [95% CI, 7.1-94.0]), ALMS1 (P=1.3×10-7; 13.0% in FSGS cases vs 0% in controls), and FGFR4 (P=4.3×10-6; OR, 24.8 [95% CI, 6.3-97.7]) genes, all of which had previously been associated with adult FSGS, kidney function, or chronic kidney disease. We also highlighted novel, functionally relevant genes, including GRB2 (which encodes a slit diaphragm protein promoting podocyte structure through actin polymerization) and ITGB1 (which is linked to renal injuries). Our results suggest a major role for immune responses and antigen presentation in pediatric FSGS through (1) associations with SNPs in PTPRJ (or CD148, P=3.5×10-7), which plays a role in T-cell receptor signaling, (2) HLA-DRB1∗11:01 association (P=6.1×10-3; OR, 4.5 [95% CI, 1.5-13.0]), and (3) signaling pathway enrichment (P=1.3×10-6). LIMITATIONS Sample size and no independent replication cohort with genomic data readily available. CONCLUSIONS Our genetic study has identified functionally relevant risk factors and the importance of immune regulation for pediatric primary FSGS, which contributes to a better description of its molecular pathophysiological mechanisms.
Collapse
Affiliation(s)
- Axelle Durand
- Center for Research in Transplantation and Translational Immunology (UMR 1064), Nantes Université, Ecole Centrale Nantes, CHU Nantes, INSERM, F-44000 Nantes, France
| | - Cheryl A Winkler
- Basic Research Laboratory, Center for Cancer Research, Frederick National Laboratory, National Cancer Institute, Frederick, Maryland
| | - Nicolas Vince
- Center for Research in Transplantation and Translational Immunology (UMR 1064), Nantes Université, Ecole Centrale Nantes, CHU Nantes, INSERM, F-44000 Nantes, France
| | - Venceslas Douillard
- Center for Research in Transplantation and Translational Immunology (UMR 1064), Nantes Université, Ecole Centrale Nantes, CHU Nantes, INSERM, F-44000 Nantes, France
| | - Estelle Geffard
- Center for Research in Transplantation and Translational Immunology (UMR 1064), Nantes Université, Ecole Centrale Nantes, CHU Nantes, INSERM, F-44000 Nantes, France
| | - Elizabeth Binns-Roemer
- Basic Research Laboratory, Center for Cancer Research, Frederick National Laboratory, National Cancer Institute, Frederick, Maryland
| | - Derek K Ng
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Pierre-Antoine Gourraud
- Center for Research in Transplantation and Translational Immunology (UMR 1064), Nantes Université, Ecole Centrale Nantes, CHU Nantes, INSERM, F-44000 Nantes, France
| | - Kimberley Reidy
- Children's Hospital at Montefiore, Albert Einstein College of Medicine, Bronx, New York
| | | | - Susan Furth
- Children's Hospital of Pennsylvania, Philadelphia, Pennsylvania
| | - Jeffrey B Kopp
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Frederick J Kaskel
- Children's Hospital at Montefiore, Albert Einstein College of Medicine, Bronx, New York
| | - Sophie Limou
- Center for Research in Transplantation and Translational Immunology (UMR 1064), Nantes Université, Ecole Centrale Nantes, CHU Nantes, INSERM, F-44000 Nantes, France.
| |
Collapse
|
2
|
Hörhold F, Eisel D, Oswald M, Kolte A, Röll D, Osen W, Eichmüller SB, König R. Reprogramming of macrophages employing gene regulatory and metabolic network models. PLoS Comput Biol 2020; 16:e1007657. [PMID: 32097424 PMCID: PMC7059956 DOI: 10.1371/journal.pcbi.1007657] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 03/06/2020] [Accepted: 01/14/2020] [Indexed: 12/20/2022] Open
Abstract
Upon exposure to different stimuli, resting macrophages undergo classical or alternative polarization into distinct phenotypes that can cause fatal dysfunction in a large range of diseases, such as systemic infection leading to sepsis or the generation of an immunosuppressive tumor microenvironment. Investigating gene regulatory and metabolic networks, we observed two metabolic switches during polarization. Most prominently, anaerobic glycolysis was utilized by M1-polarized macrophages, while the biosynthesis of inosine monophosphate was upregulated in M2-polarized macrophages. Moreover, we observed a switch in the urea cycle. Gene regulatory network models revealed E2F1, MYC, PPARγ and STAT6 to be the major players in the distinct signatures of these polarization events. Employing functional assays targeting these regulators, we observed the repolarization of M2-like cells into M1-like cells, as evidenced by their specific gene expression signatures and cytokine secretion profiles. The predicted regulators are essential to maintaining the M2-like phenotype and function and thus represent potential targets for the therapeutic reprogramming of immunosuppressive M2-like macrophages.
Collapse
Affiliation(s)
- Franziska Hörhold
- Center for Sepsis Control and Care, University Hospital, Jena, Germany
| | - David Eisel
- Research Group GMP & T Cell Therapy, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Biopharmaceutical New Technologies (BioNTech) Corporation, Mainz, Germany
| | - Marcus Oswald
- Center for Sepsis Control and Care, University Hospital, Jena, Germany
| | - Amol Kolte
- Center for Sepsis Control and Care, University Hospital, Jena, Germany
| | - Daniela Röll
- Center for Sepsis Control and Care, University Hospital, Jena, Germany
| | - Wolfram Osen
- Research Group GMP & T Cell Therapy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan B. Eichmüller
- Research Group GMP & T Cell Therapy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rainer König
- Center for Sepsis Control and Care, University Hospital, Jena, Germany
| |
Collapse
|
3
|
Poos AM, Kordaß T, Kolte A, Ast V, Oswald M, Rippe K, König R. Modelling TERT regulation across 19 different cancer types based on the MIPRIP 2.0 gene regulatory network approach. BMC Bioinformatics 2019; 20:737. [PMID: 31888467 PMCID: PMC6937852 DOI: 10.1186/s12859-019-3323-2] [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: 11/12/2019] [Accepted: 12/16/2019] [Indexed: 01/15/2023] Open
Abstract
Background Reactivation of the telomerase reverse transcriptase gene TERT is a central feature for unlimited proliferation of the majority of cancers. However, the underlying regulatory processes are only partly understood. Results We assembled regulator binding information from serveral sources to construct a generic human and mouse gene regulatory network. Advancing our “Mixed Integer linear Programming based Regulatory Interaction Predictor” (MIPRIP) approach, we identified the most common and cancer-type specific regulators of TERT across 19 different human cancers. The results were validated by using the well-known TERT regulation by the ETS1 transcription factor in a subset of melanomas with mutations in the TERT promoter. Our improved MIPRIP2 R-package and the associated generic regulatory networks are freely available at https://github.com/KoenigLabNM/MIPRIP. Conclusion MIPRIP 2.0 identified common as well as tumor type specific regulators of TERT. The software can be easily applied to transcriptome datasets to predict gene regulation for any gene and disease/condition under investigation.
Collapse
Affiliation(s)
- Alexandra M Poos
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany.,Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Theresa Kordaß
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,Research Group GMP & T Cell Therapy, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Amol Kolte
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Volker Ast
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Marcus Oswald
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany
| | - Rainer König
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany.
| |
Collapse
|
4
|
Garcia-Alonso L, Holland CH, Ibrahim MM, Turei D, Saez-Rodriguez J. Benchmark and integration of resources for the estimation of human transcription factor activities. Genome Res 2019; 29:1363-1375. [PMID: 31340985 PMCID: PMC6673718 DOI: 10.1101/gr.240663.118] [Citation(s) in RCA: 411] [Impact Index Per Article: 82.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 05/28/2019] [Indexed: 12/25/2022]
Abstract
The prediction of transcription factor (TF) activities from the gene expression of their targets (i.e., TF regulon) is becoming a widely used approach to characterize the functional status of transcriptional regulatory circuits. Several strategies and data sets have been proposed to link the target genes likely regulated by a TF, each one providing a different level of evidence. The most established ones are (1) manually curated repositories, (2) interactions derived from ChIP-seq binding data, (3) in silico prediction of TF binding on gene promoters, and (4) reverse-engineered regulons from large gene expression data sets. However, it is not known how these different sources of regulons affect the TF activity estimations and, thereby, downstream analysis and interpretation. Here we compared the accuracy and biases of these strategies to define human TF regulons by means of their ability to predict changes in TF activities in three reference benchmark data sets. We assembled a collection of TF-target interactions for 1541 human TFs and evaluated how different molecular and regulatory properties of the TFs, such as the DNA-binding domain, specificities, or mode of interaction with the chromatin, affect the predictions of TF activity. We assessed their coverage and found little overlap on the regulons derived from each strategy and better performance by literature-curated information followed by ChIP-seq data. We provide an integrated resource of all TF-target interactions derived through these strategies, with confidence scores, as a resource for enhanced prediction of TF activities.
Collapse
Affiliation(s)
- Luz Garcia-Alonso
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, CB10 1SD Cambridge, United Kingdom
- Open Targets, Wellcome Genome Campus, CB10 1SD Cambridge, United Kingdom
| | - Christian H Holland
- Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Faculty of Medicine, 52074 Aachen, Germany
- Institute of Computational Biomedicine, Heidelberg University, Faculty of Medicine, 69120 Heidelberg, Germany
| | - Mahmoud M Ibrahim
- Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Faculty of Medicine, 52074 Aachen, Germany
- Department of Nephrology, RWTH Aachen University, Faculty of Medicine, 52074 Aachen, Germany
| | - Denes Turei
- Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Faculty of Medicine, 52074 Aachen, Germany
- Institute of Computational Biomedicine, Heidelberg University, Faculty of Medicine, 69120 Heidelberg, Germany
| | - Julio Saez-Rodriguez
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, CB10 1SD Cambridge, United Kingdom
- Open Targets, Wellcome Genome Campus, CB10 1SD Cambridge, United Kingdom
- Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Faculty of Medicine, 52074 Aachen, Germany
- Institute of Computational Biomedicine, Heidelberg University, Faculty of Medicine, 69120 Heidelberg, Germany
| |
Collapse
|
5
|
Artigas-Jerónimo S, Estrada-Peña A, Cabezas-Cruz A, Alberdi P, Villar M, de la Fuente J. Modeling Modulation of the Tick Regulome in Response to Anaplasma phagocytophilum for the Identification of New Control Targets. Front Physiol 2019; 10:462. [PMID: 31057429 PMCID: PMC6482211 DOI: 10.3389/fphys.2019.00462] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/04/2019] [Indexed: 12/31/2022] Open
Abstract
Ticks act as vectors of pathogens affecting human and animal health worldwide, and recent research has focused on the characterization of tick-pathogen interactions using omics technologies to identify new targets for developing novel control interventions. The regulome (transcription factors-target genes interactions) plays a critical role in cell response to pathogen infection. Therefore, the application of regulomics to tick-pathogen interactions would advance our understanding of these molecular interactions and contribute to the identification of novel control targets for the prevention and control of tick infestations and tick-borne diseases. However, limited information is available on the role of tick regulome in response to pathogen infection. In this study, we applied complementary in silico approaches to modeling how Anaplasma phagocytophilum infection modulates tick vector regulome. This proof-of-concept research provided support for the use of network analysis in the study of regulome response to infection, resulting in new information on tick-pathogen interactions and potential targets for developing interventions for the control of tick infestations and pathogen transmission. Deciphering the precise nature of circuits that shape the tick regulome in response to pathogen infection is an area of research that in the future will advance our knowledge of tick-pathogen interactions, and the identification of new antigens for the control of tick infestations and pathogen infection/transmission.
Collapse
Affiliation(s)
- Sara Artigas-Jerónimo
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ciudad Real, Spain
| | | | - Alejandro Cabezas-Cruz
- UMR BIPAR, INRA, ANSES, Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, Maisons-Alfort, France
| | - Pilar Alberdi
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ciudad Real, Spain
| | - Margarita Villar
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ciudad Real, Spain
| | - José de la Fuente
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ciudad Real, Spain.,Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, United States
| |
Collapse
|
6
|
Zhou Y, Zhu W, Zhang L, Zeng Y, Xu C, Tian Q, Deng HW. Transcriptomic Data Identified Key Transcription Factors for Osteoporosis in Caucasian Women. Calcif Tissue Int 2018; 103:581-588. [PMID: 30056508 PMCID: PMC6343666 DOI: 10.1007/s00223-018-0457-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 07/14/2018] [Indexed: 12/27/2022]
Abstract
Osteoporosis is a prevalent bone metabolic disease, mainly caused by excessive bone resorption (by osteoclasts) over bone formation (by osteoblasts). Identifying the key transcription factors and understanding the regulatory network influencing osteoclastogenesis will be helpful to explore the potential biological mechanism for osteoporosis. In our study, peripheral blood monocyte (PBM) was used as a cell model for bone mineral density (BMD) research. PBMs serve as progenitors of osteoclasts and produce important cytokines for osteoclastogenesis. In our study, via exon arrays, gene expression profiles of PBMs were analyzed between high versus low hip BMD groups. Transcription factors for differentially expressed genes were then predicted based on the enrichment analysis. We found that 591 genes were differentially expressed between the two BMD groups (nominally significant, raw p value < 0.05). For high BMD subjects, 482 genes were up-regulated and 109 genes were down-regulated. We then found 29 potential transcription factors for up-regulated genes and nine transcription factors for down-regulated genes. Among these transcription factors, HMGA1 and NFKB2 were differentially expressed between high versus low BMD groups. In addition, their regulation types with their target genes were consistent with the information from public databases. Our findings of key transcription factors and their target genes for osteoporosis were further validated by GWAS analysis. Overall, we predicted important transcription factors for osteoporosis. We were also able to infer the regulatory mechanism that exists between transcription factors and target genes in bone metabolism.
Collapse
Affiliation(s)
- Yu Zhou
- Center of Genomics and Bioinformatics, Tulane University, New Orleans, LA, 70112, USA
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA, 70118, USA
| | - Wei Zhu
- Center of Genomics and Bioinformatics, Tulane University, New Orleans, LA, 70112, USA
- Department of Biostatistics and Bioinformatics, Tulane University, New Orleans, LA, 70112, USA
| | - Lan Zhang
- Center of Genomics and Bioinformatics, Tulane University, New Orleans, LA, 70112, USA
- Department of Biostatistics and Bioinformatics, Tulane University, New Orleans, LA, 70112, USA
| | - Yong Zeng
- Center of Genomics and Bioinformatics, Tulane University, New Orleans, LA, 70112, USA
- Department of Biostatistics and Bioinformatics, Tulane University, New Orleans, LA, 70112, USA
| | - Chao Xu
- Center of Genomics and Bioinformatics, Tulane University, New Orleans, LA, 70112, USA
- Department of Biostatistics and Bioinformatics, Tulane University, New Orleans, LA, 70112, USA
| | - Qing Tian
- Center of Genomics and Bioinformatics, Tulane University, New Orleans, LA, 70112, USA
- Department of Biostatistics and Bioinformatics, Tulane University, New Orleans, LA, 70112, USA
| | - Hong-Wen Deng
- Center of Genomics and Bioinformatics, Tulane University, New Orleans, LA, 70112, USA.
- Department of Biostatistics and Bioinformatics, Tulane University, New Orleans, LA, 70112, USA.
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University, 1440 Canal St., RM 1619F, New Orleans, LA, 70112, USA.
| |
Collapse
|
7
|
Vafaee F, Diakos C, Kirschner MB, Reid G, Michael MZ, Horvath LG, Alinejad-Rokny H, Cheng ZJ, Kuncic Z, Clarke S. A data-driven, knowledge-based approach to biomarker discovery: application to circulating microRNA markers of colorectal cancer prognosis. NPJ Syst Biol Appl 2018; 4:20. [PMID: 29872543 PMCID: PMC5981448 DOI: 10.1038/s41540-018-0056-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 04/11/2018] [Accepted: 05/04/2018] [Indexed: 02/08/2023] Open
Abstract
Recent advances in high-throughput technologies have provided an unprecedented opportunity to identify molecular markers of disease processes. This plethora of complex-omics data has simultaneously complicated the problem of extracting meaningful molecular signatures and opened up new opportunities for more sophisticated integrative and holistic approaches. In this era, effective integration of data-driven and knowledge-based approaches for biomarker identification has been recognised as key to improving the identification of high-performance biomarkers, and necessary for translational applications. Here, we have evaluated the role of circulating microRNA as a means of predicting the prognosis of patients with colorectal cancer, which is the second leading cause of cancer-related death worldwide. We have developed a multi-objective optimisation method that effectively integrates a data-driven approach with the knowledge obtained from the microRNA-mediated regulatory network to identify robust plasma microRNA signatures which are reliable in terms of predictive power as well as functional relevance. The proposed multi-objective framework has the capacity to adjust for conflicting biomarker objectives and to incorporate heterogeneous information facilitating systems approaches to biomarker discovery. We have found a prognostic signature of colorectal cancer comprising 11 circulating microRNAs. The identified signature predicts the patients' survival outcome and targets pathways underlying colorectal cancer progression. The altered expression of the identified microRNAs was confirmed in an independent public data set of plasma samples of patients in early stage vs advanced colorectal cancer. Furthermore, the generality of the proposed method was demonstrated across three publicly available miRNA data sets associated with biomarker studies in other diseases.
Collapse
Affiliation(s)
- Fatemeh Vafaee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2033 Australia
| | - Connie Diakos
- Kolling Institute of Medical Research, University of Sydney, Royal North Shore Hospital, Reserve Road, St Leonards, NSW 2065 Australia
| | | | - Glen Reid
- Asbestos Diseases Research Institute, Hospital Road, Concord, NSW 2139 Australia
- Sydney Medical School, University of Sydney, Sydney, NSW 2050 Australia
| | - Michael Z. Michael
- Flinders Centre for Innovation in Cancer, Flinders Medical Centre, Flinders University, Adelaide, SA 5042 Australia
| | - Lisa G. Horvath
- Sydney Medical School, University of Sydney, Sydney, NSW 2050 Australia
- Chris O’Brien Lifehouse, Missenden Road, Camperdown, NSW 2050 Australia
- Royal Prince Alfred Hospital, Camperdown, NSW 2050 Australia
| | | | - Zhangkai Jason Cheng
- Charles Perkins Centre, University of Sydney, Sydney, NSW 2006 Australia
- School of Physics, University of Sydney, Sydney, NSW 2006 Australia
| | - Zdenka Kuncic
- Charles Perkins Centre, University of Sydney, Sydney, NSW 2006 Australia
- School of Physics, University of Sydney, Sydney, NSW 2006 Australia
| | - Stephen Clarke
- Kolling Institute of Medical Research, University of Sydney, Royal North Shore Hospital, Reserve Road, St Leonards, NSW 2065 Australia
| |
Collapse
|
8
|
Lemmelä S, Solovieva S, Shiri R, Benner C, Heliövaara M, Kettunen J, Anttila V, Ripatti S, Perola M, Seppälä I, Juonala M, Kähönen M, Salomaa V, Viikari J, Raitakari OT, Lehtimäki T, Palotie A, Viikari-Juntura E, Husgafvel-Pursiainen K. Genome-Wide Meta-Analysis of Sciatica in Finnish Population. PLoS One 2016; 11:e0163877. [PMID: 27764105 PMCID: PMC5072673 DOI: 10.1371/journal.pone.0163877] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 09/15/2016] [Indexed: 12/14/2022] Open
Abstract
Sciatica or the sciatic syndrome is a common and often disabling low back disorder in the working-age population. It has a relatively high heritability but poorly understood molecular mechanisms. The Finnish population is a genetic isolate where small founder population and bottleneck events have led to enrichment of certain rare and low frequency variants. We performed here the first genome-wide association (GWAS) and meta-analysis of sciatica. The meta-analysis was conducted across two GWAS covering 291 Finnish sciatica cases and 3671 controls genotyped and imputed at 7.7 million autosomal variants. The most promising loci (p<1x10-6) were replicated in 776 Finnish sciatica patients and 18,489 controls. We identified five intragenic variants, with relatively low frequencies, at two novel loci associated with sciatica at genome-wide significance. These included chr9:14344410:I (rs71321981) at 9p22.3 (NFIB gene; p = 1.30x10-8, MAF = 0.08) and four variants at 15q21.2: rs145901849, rs80035109, rs190200374 and rs117458827 (MYO5A; p = 1.34x10-8, MAF = 0.06; p = 2.32x10-8, MAF = 0.07; p = 3.85x10-8, MAF = 0.06; p = 4.78x10-8, MAF = 0.07, respectively). The most significant association in the meta-analysis, a single base insertion rs71321981 within the regulatory region of the transcription factor NFIB, replicated in an independent Finnish population sample (p = 0.04). Despite identifying 15q21.2 as a promising locus, we were not able to replicate it. It was differentiated; the lead variants within 15q21.2 were more frequent in Finland (6–7%) than in other European populations (1–2%). Imputation accuracies of the three significantly associated variants (chr9:14344410:I, rs190200374, and rs80035109) were validated by genotyping. In summary, our results suggest a novel locus, 9p22.3 (NFIB), which may be involved in susceptibility to sciatica. In addition, another locus, 15q21.2, emerged as a promising one, but failed to replicate.
Collapse
Affiliation(s)
- Susanna Lemmelä
- Health and Work Ability, Finnish Institute of Occupational Health, 00250 Helsinki, Finland
| | - Svetlana Solovieva
- Health and Work Ability, Finnish Institute of Occupational Health, 00250 Helsinki, Finland
| | - Rahman Shiri
- Health and Work Ability, Finnish Institute of Occupational Health, 00250 Helsinki, Finland
| | - Christian Benner
- Institute for Molecular Medicine Finland (FIMM), 00014 University of Helsinki, Helsinki, Finland
- Department of Public Health, 00014 University of Helsinki, Helsinki, Finland
| | - Markku Heliövaara
- Population Health Unit, National Institute for Health and Welfare, 00251 Helsinki, Finland
| | - Johannes Kettunen
- Faculty of Medicine, Institute of Health Sciences, University of Oulu, 90220 Oulu, Finland
- NMR Metabolomics Laboratory, University of Eastern Finland, Kuopio, Finland
- National Institute for Health and Welfare, Helsinki, Finland
| | - Verneri Anttila
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States of America
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), 00014 University of Helsinki, Helsinki, Finland
- Department of Public Health, 00014 University of Helsinki, Helsinki, Finland
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, United Kingdom
| | - Markus Perola
- Institute for Molecular Medicine Finland (FIMM), 00014 University of Helsinki, Helsinki, Finland
- Public Health Genomics Unit, Department of Chronic Disease Prevention, National Institute for Health and Welfare, 00271 Helsinki, Finland
- The Estonian Genome Center, University of Tartu, 51010 Tartu, Estonia
| | - Ilkka Seppälä
- Department of Clinical Chemistry, Fimlab Laboratories, University of Tampere School of Medicine, 33520 Tampere, Finland
| | - Markus Juonala
- Division of Medicine, Turku University Hospital, 20521 Turku, Finland
- Department of Medicine, University of Turku, 20521 Turku, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, 33521 Tampere, Finland
| | - Veikko Salomaa
- Department of Health, National Institute for Health and Welfare, 00251 Helsinki, Finland
| | - Jorma Viikari
- Division of Medicine, Turku University Hospital, 20521 Turku, Finland
- Department of Medicine, University of Turku, 20521 Turku, Finland
| | - Olli T. Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, 20520 Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, 20521 Turku, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, University of Tampere School of Medicine, 33520 Tampere, Finland
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), 00014 University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States of America
- Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts 02114, United States of America
| | - Eira Viikari-Juntura
- Disability Prevention Centre, Finnish Institute of Occupational Health, 00250 Helsinki, Finland
| | | |
Collapse
|
9
|
Vafaee F, Krycer JR, Ma X, Burykin T, James DE, Kuncic Z. ORTI: An Open-Access Repository of Transcriptional Interactions for Interrogating Mammalian Gene Expression Data. PLoS One 2016; 11:e0164535. [PMID: 27723773 PMCID: PMC5056720 DOI: 10.1371/journal.pone.0164535] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 09/27/2016] [Indexed: 12/11/2022] Open
Abstract
Transcription factors (TFs) play a fundamental role in coordinating biological processes in response to stimuli. Consequently, we often seek to determine the key TFs and their regulated target genes (TGs) amidst gene expression data. This requires a knowledge-base of TF-TG interactions, which would enable us to determine the topology of the transcriptional network and predict novel regulatory interactions. To address this, we generated an Open-access Repository of Transcriptional Interactions, ORTI, by integrating available TF-TG interaction databases. These databases rely on different types of experimental evidence, including low-throughput assays, high-throughput screens, and bioinformatics predictions. We have subsequently categorised TF-TG interactions in ORTI according to the quality of this evidence. To demonstrate its capabilities, we applied ORTI to gene expression data and identified modulated TFs using an enrichment analysis. Combining this with pairwise TF-TG interactions enabled us to visualise temporal regulation of a transcriptional network. Additionally, ORTI enables the prediction of novel TF-TG interactions, based on how well candidate genes co-express with known TGs of the target TF. By filtering out known TF-TG interactions that are unlikely to occur within the experimental context, this analysis predicts context-specific TF-TG interactions. We show that this can be applied to experimental designs of varying complexities. In conclusion, ORTI is a rich and publicly available database of experimentally validated mammalian transcriptional interactions which is accompanied with tools that can identify and predict transcriptional interactions, serving as a useful resource for unravelling the topology of transcriptional networks.
Collapse
Affiliation(s)
- Fatemeh Vafaee
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, Australia
- * E-mail: (FV); (ZK)
| | - James R. Krycer
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Xiuquan Ma
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- Diabetes and Metabolism Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia
| | - Timur Burykin
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - David E. James
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Zdenka Kuncic
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- School of Physics, The University of Sydney, Sydney, NSW, Australia
- * E-mail: (FV); (ZK)
| |
Collapse
|
10
|
Verma SS, Frase AT, Verma A, Pendergrass SA, Mahony S, Haas DW, Ritchie MD. PHENOME-WIDE INTERACTION STUDY (PheWIS) IN AIDS CLINICAL TRIALS GROUP DATA (ACTG). PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2016; 21:57-68. [PMID: 26776173 PMCID: PMC4722952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Association studies have shown and continue to show a substantial amount of success in identifying links between multiple single nucleotide polymorphisms (SNPs) and phenotypes. These studies are also believed to provide insights toward identification of new drug targets and therapies. Albeit of all the success, challenges still remain for applying and prioritizing these associations based on available biological knowledge. Along with single variant association analysis, genetic interactions also play an important role in uncovering the etiology and progression of complex traits. For gene-gene interaction analysis, selection of the variants to test for associations still poses a challenge in identifying epistatic interactions among the large list of variants available in high-throughput, genome-wide datasets. Therefore in this study, we propose a pipeline to identify interactions among genetic variants that are associated with multiple phenotypes by prioritizing previously published results from main effect association analysis (genome-wide and phenome-wide association analysis) based on a-priori biological knowledge in AIDS Clinical Trials Group (ACTG) data. We approached the prioritization and filtration of variants by using the results of a previously published single variant PheWAS and then utilizing biological information from the Roadmap Epigenome project. We removed variants in low functional activity regions based on chromatin states annotation and then conducted an exhaustive pairwise interaction search using linear regression analysis. We performed this analysis in two independent pre-treatment clinical trial datasets from ACTG to allow for both discovery and replication. Using a regression framework, we observed 50,798 associations that replicate at p-value 0.01 for 26 phenotypes, among which 2,176 associations for 212 unique SNPs for fasting blood glucose phenotype reach Bonferroni significance and an additional 9,970 interactions for high-density lipoprotein (HDL) phenotype and fasting blood glucose (total of 12,146 associations) reach FDR significance. We conclude that this method of prioritizing variants to look for epistatic interactions can be used extensively for generating hypotheses for genomewide and phenome-wide interaction analyses. This original Phenome-wide Interaction study (PheWIS) can be applied further to patients enrolled in randomized clinical trials to establish the relationship between patient's response to a particular drug therapy and non-linear combination of variants that might be affecting the outcome.
Collapse
Affiliation(s)
- Shefali S Verma
- Center for System Genomics, The Pennsylvania State University, University Park, PA 16802, USA
| | | | | | | | | | | | | |
Collapse
|
11
|
Lesurf R, Cotto KC, Wang G, Griffith M, Kasaian K, Jones SJM, Montgomery SB, Griffith OL. ORegAnno 3.0: a community-driven resource for curated regulatory annotation. Nucleic Acids Res 2015; 44:D126-32. [PMID: 26578589 PMCID: PMC4702855 DOI: 10.1093/nar/gkv1203] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 10/26/2015] [Indexed: 12/26/2022] Open
Abstract
The Open Regulatory Annotation database (ORegAnno) is a resource for curated regulatory annotation. It contains information about regulatory regions, transcription factor binding sites, RNA binding sites, regulatory variants, haplotypes, and other regulatory elements. ORegAnno differentiates itself from other regulatory resources by facilitating crowd-sourced interpretation and annotation of regulatory observations from the literature and highly curated resources. It contains a comprehensive annotation scheme that aims to describe both the elements and outcomes of regulatory events. Moreover, ORegAnno assembles these disparate data sources and annotations into a single, high quality catalogue of curated regulatory information. The current release is an update of the database previously featured in the NAR Database Issue, and now contains 1 948 307 records, across 18 species, with a combined coverage of 334 215 080 bp. Complete records, annotation, and other associated data are available for browsing and download at http://www.oreganno.org/.
Collapse
Affiliation(s)
- Robert Lesurf
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Kelsy C Cotto
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Grace Wang
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Malachi Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Katayoon Kasaian
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Stephen B Montgomery
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Obi L Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | |
Collapse
|
12
|
Sleeping Beauty mutagenesis in a mouse medulloblastoma model defines networks that discriminate between human molecular subgroups. Proc Natl Acad Sci U S A 2013; 110:E4325-34. [PMID: 24167280 DOI: 10.1073/pnas.1318639110] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The Sleeping Beauty (SB) transposon mutagenesis screen is a powerful tool to facilitate the discovery of cancer genes that drive tumorigenesis in mouse models. In this study, we sought to identify genes that functionally cooperate with sonic hedgehog signaling to initiate medulloblastoma (MB), a tumor of the cerebellum. By combining SB mutagenesis with Patched1 heterozygous mice (Ptch1(lacZ/+)), we observed an increased frequency of MB and decreased tumor-free survival compared with Ptch1(lacZ/+) controls. From an analysis of 85 tumors, we identified 77 common insertion sites that map to 56 genes potentially driving increased tumorigenesis. The common insertion site genes identified in the mutagenesis screen were mapped to human orthologs, which were used to select probes and corresponding expression data from an independent set of previously described human MB samples, and surprisingly were capable of accurately clustering known molecular subgroups of MB, thereby defining common regulatory networks underlying all forms of MB irrespective of subgroup. We performed a network analysis to discover the likely mechanisms of action of subnetworks and used an in vivo model to confirm a role for a highly ranked candidate gene, Nfia, in promoting MB formation. Our analysis implicates candidate cancer genes in the deregulation of apoptosis and translational elongation, and reveals a strong signature of transcriptional regulation that will have broad impact on expression programs in MB. These networks provide functional insights into the complex biology of human MB and identify potential avenues for intervention common to all clinical subgroups.
Collapse
|