1
|
Mørup SB, Leung P, Reilly C, Sherman BT, Chang W, Milojevic M, Milinkovic A, Liappis A, Borgwardt L, Petoumenos K, Paredes R, Mistry SS, MacPherson CR, Lundgren J, Helleberg M, Reekie J, Murray DD. The association between single-nucleotide polymorphisms within type 1 interferon pathway genes and human immunodeficiency virus type 1 viral load in antiretroviral-naïve participants. AIDS Res Ther 2024; 21:27. [PMID: 38698440 PMCID: PMC11067292 DOI: 10.1186/s12981-024-00610-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/29/2024] [Indexed: 05/05/2024] Open
Abstract
BACKGROUND Human genetic contribution to HIV progression remains inadequately explained. The type 1 interferon (IFN) pathway is important for host control of HIV and variation in type 1 IFN genes may contribute to disease progression. This study assessed the impact of variations at the gene and pathway level of type 1 IFN on HIV-1 viral load (VL). METHODS Two cohorts of antiretroviral (ART) naïve participants living with HIV (PLWH) with either early (START) or advanced infection (FIRST) were analysed separately. Type 1 IFN genes (n = 17) and receptor subunits (IFNAR1, IFNAR2) were examined for both cumulated type 1 IFN pathway analysis and individual gene analysis. SKAT-O was applied to detect associations between the genotype and HIV-1 study entry viral load (log10 transformed) as a proxy for set point VL; P-values were corrected using Bonferroni (P < 0.0025). RESULTS The analyses among those with early infection included 2429 individuals from five continents. The median study entry HIV VL was 14,623 (IQR 3460-45100) copies/mL. Across 673 SNPs within 19 type 1 IFN genes, no significant association with study entry VL was detected. Conversely, examining individual genes in START showed a borderline significant association between IFNW1, and study entry VL (P = 0.0025). This significance remained after separate adjustments for age, CD4+ T-cell count, CD4+/CD8+ T-cell ratio and recent infection. When controlling for population structure using linear mixed effects models (LME), in addition to principal components used in the main model, this was no longer significant (p = 0.0244). In subgroup analyses stratified by geographical region, the association between IFNW1 and study entry VL was only observed among African participants, although, the association was not significant when controlling for population structure using LME. Of the 17 SNPs within the IFNW1 region, only rs79876898 (A > G) was associated with study entry VL (p = 0.0020, beta = 0.32; G associated with higher study entry VL than A) in single SNP association analyses. The findings were not reproduced in FIRST participants. CONCLUSION Across 19 type 1 IFN genes, only IFNW1 was associated with HIV-1 study entry VL in a cohort of ART-naïve individuals in early stages of their infection, however, this was no longer significant in sensitivity analyses that controlled for population structures using LME.
Collapse
Affiliation(s)
- Sara Bohnstedt Mørup
- Centre of Excellence for Health, Immunity, and Infections, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Preston Leung
- Centre of Excellence for Health, Immunity, and Infections, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Cavan Reilly
- Division of Biostatistics and Health Data Science, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Brad T Sherman
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Weizhong Chang
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Maja Milojevic
- Centre of Excellence for Health, Immunity, and Infections, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Ana Milinkovic
- Chelsea and Westminster Hospital NHS Foundation Trust, London, UK
| | - Angelike Liappis
- Washington DC Veterans Affairs Medical Center and The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Line Borgwardt
- Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Kathy Petoumenos
- Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Roger Paredes
- Department of Infectious Diseases and IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Shweta S Mistry
- Division of Biostatistics and Health Data Science, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Cameron R MacPherson
- Centre of Excellence for Health, Immunity, and Infections, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Institut Roche, Boulogne-Billancourt, France
| | - Jens Lundgren
- Centre of Excellence for Health, Immunity, and Infections, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Marie Helleberg
- Centre of Excellence for Health, Immunity, and Infections, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Joanne Reekie
- Centre of Excellence for Health, Immunity, and Infections, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Daniel D Murray
- Centre of Excellence for Health, Immunity, and Infections, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.
| |
Collapse
|
2
|
dos Santos Q, Leung P, Thorball CW, Ledergerber B, Fellay J, MacPherson CR, Hornum M, Terrones-Campos C, Rasmussen A, Gustafsson F, Perch M, Sørensen SS, Ekenberg C, Lundgren JD, Feldt‐Rasmussen B, Reekie J. Predicting type 2 diabetes risk before and after solid organ transplantation using polygenic scores in a Danish cohort. Front Mol Biosci 2023; 10:1282412. [PMID: 38131015 PMCID: PMC10733470 DOI: 10.3389/fmolb.2023.1282412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Type 2 diabetes mellitus (T2DM) can be multifactorial where both genetics and environmental factors play a role. We aimed to investigate the use of polygenic risk scores (PRS) in the prediction of pre-transplant T2DM and post-transplant diabetes mellitus (PTDM) among solid organ transplant (SOT) patients. Using non-genetic risk scores alone; and the combination with PRS, separate logistic regression models were built and compared using receiver operator curves. Patients were assessed pre-transplant and in three post-transplant periods: 0-45, 46-365 and >365 days. A higher PRS was significantly associated with increased odds of pre-transplant T2DM. However, no improvement was observed for pre-transplant T2DM prediction when comparing PRS combined with non-genetic risk scores to using non-genetic risk scores alone. This was also true for predictions of PTDM in all three post-transplant periods. This study demonstrated that polygenic risk was only associated with the risk of T2DM among SOT recipients prior to transplant and not for PTDM. Combining PRS with a clinical model of non-genetic risk scores did not significantly improve the predictive ability, indicating its limited clinical utility in identifying patients at high risk for T2DM before transplantation, suggesting that non-genetic or different genetic factors may contribute to PTDM.
Collapse
Affiliation(s)
- Quenia dos Santos
- Centre of Excellence for Health, Institut Roche, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Preston Leung
- Centre of Excellence for Health, Institut Roche, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Christian W. Thorball
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Bruno Ledergerber
- Centre of Excellence for Health, Institut Roche, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Jacques Fellay
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Cameron R. MacPherson
- Centre of Excellence for Health, Institut Roche, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Institut Roche, Boulogne-Billancourt, France
| | - Mads Hornum
- Department of Nephrology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Cynthia Terrones-Campos
- Centre of Excellence for Health, Institut Roche, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Allan Rasmussen
- Department of Surgical Gastroenterology, Rigshospitalet, Copenhagen, Denmark
| | - Finn Gustafsson
- Department of Cardiology, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael Perch
- Department of Cardiology, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren S. Sørensen
- Department of Nephrology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Christina Ekenberg
- Centre of Excellence for Health, Institut Roche, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Jens D. Lundgren
- Centre of Excellence for Health, Institut Roche, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Bo Feldt‐Rasmussen
- Department of Nephrology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Joanne Reekie
- Centre of Excellence for Health, Institut Roche, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
3
|
Zucco AG, Bennedbæk M, Ekenberg C, Gabrielaite M, Leung P, Polizzotto MN, Kan V, Murray DD, Lundgren JD, MacPherson CR. Associations of functional human leucocyte antigen class I groups with HIV viral load in a heterogeneous cohort. AIDS 2023; 37:1643-1650. [PMID: 37534724 PMCID: PMC10399941 DOI: 10.1097/qad.0000000000003557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 03/13/2023] [Accepted: 03/21/2023] [Indexed: 04/07/2023]
Abstract
OBJECTIVE Human leucocyte antigen (HLA) class I alleles are the main host genetic factors involved in controlling HIV-1 viral load (VL). Nevertheless, HLA diversity has proven a significant challenge in association studies. We assessed how accounting for binding affinities of HLA class I alleles to HIV-1 peptides facilitate association testing of HLA with HIV-1 VL in a heterogeneous cohort. DESIGN Cohort from the Strategic Timing of AntiRetroviral Treatment (START) study. METHODS We imputed HLA class I alleles from host genetic data (2546 HIV+ participants) and sampled immunopeptidomes from 2079 host-paired viral genomes (targeted amplicon sequencing). We predicted HLA class I binding affinities to HIV-1 and unspecific peptides, grouping alleles into functional clusters through consensus clustering. These functional HLA class I clusters were used to test associations with HIV VL. RESULTS We identified four clades totaling 30 HLA alleles accounting for 11.4% variability in VL. We highlight HLA-B∗57:01 and B∗57:03 as functionally similar but yet overrepresented in distinct ethnic groups, showing when combined a protective association with HIV+ VL (log, β -0.25; adj. P-value < 0.05). We further demonstrate only a slight power reduction when using unspecific immunopeptidomes, facilitating the use of the inferred functional HLA groups in other studies. CONCLUSION The outlined computational approach provides a robust and efficient way to incorporate HLA function and peptide diversity, aiding clinical association studies in heterogeneous cohorts. To facilitate access to the proposed methods and results we provide an interactive application for exploring data.
Collapse
Affiliation(s)
| | - Marc Bennedbæk
- Virus Research and Development Laboratory, Virus and Microbiological Special Diagnostics, Statens Serum Institut
| | | | - Migle Gabrielaite
- Center for Genomic Medicine, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Mark N. Polizzotto
- Clinical Hub for Interventional Research, College of Health and Medicine, The Australian National University, Canberra, Australia
| | - Virginia Kan
- George Washington University, Veterans Affairs Medical Center, Washington, DC, USA
| | | | | | | |
Collapse
|
4
|
Murray DD, Grund B, MacPherson CR, Ekenberg C, Zucco AG, Reekie J, Dominguez-Dominguez L, Leung P, Fusco D, Gras J, Gerstoft J, Helleberg M, Borges ÁH, Polizzotto MN, Lundgren JD. Association between ten-eleven methylcytosine dioxygenase 2 genetic variation and viral load in people with HIV. AIDS 2023; 37:379-387. [PMID: 36473831 PMCID: PMC9894145 DOI: 10.1097/qad.0000000000003427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 09/29/2022] [Accepted: 11/02/2022] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Identifying genetic factors that influence HIV-pathogenesis is critical for understanding disease pathways. Previous studies have suggested a role for the human gene ten-eleven methylcytosine dioxygenase 2 (TET2) in modulating HIV-pathogenesis. METHODS We assessed whether genetic variation in TET2 was associated with markers of HIV-pathogenesis using both gene level and single nucleotide polymorphism (SNP) level association in 8512 HIV-positive persons across five clinical trial cohorts. RESULTS Variation at both the gene and SNP-level of TET2 was found to be associated with levels of HIV viral load (HIV-VL) consistently in the two cohorts that recruited antiretroviral-naïve participants. The SNPs occurred in two clusters of high linkage disequilibrium (LD), one associated with high HIV-VL and the other low HIV-VL, and were predominantly found in Black participants. CONCLUSION Genetic variation in TET2 was associated with HIV-VL in two large antiretroviral therapy (ART)-naive clinical trial cohorts. The role of TET2 in HIV-pathogenesis warrants further investigation.
Collapse
Affiliation(s)
- Daniel D. Murray
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Birgit Grund
- School of Statistics, University of Minnesota, Minneapolis, MN, USA
| | - Cameron R. MacPherson
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Christina Ekenberg
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Adrian G. Zucco
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Joanne Reekie
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Lourdes Dominguez-Dominguez
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Preston Leung
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Dahlene Fusco
- Tulane University Medical Center, Tulane University, New Orleans, LA, USA
| | - Julien Gras
- Service de Maladies infectieuses et tropicales, APHP-Hôpital Saint Louis, Paris, France
| | - Jan Gerstoft
- Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet
| | - Marie Helleberg
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet
| | - Álvaro H. Borges
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases Immunology, Statens Serum Institut, Copenhagen, Denmark
| | - Mark N. Polizzotto
- Clinical Hub for Interventional Research, College of Health and Medicine, The Australian National University, Canberra, Australia
| | - Jens D. Lundgren
- Centre of Excellence for Health, Immunity and Infections (CHIP), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
5
|
Faitová T, Svanberg R, Da Cunha-Bang C, Ilett EE, Jørgensen M, Noguera-Julian M, Paredes R, MacPherson CR, Niemann CU. The gut microbiome in patients with chronic lymphocytic leukemia. Haematologica 2022; 107:2238-2243. [PMID: 35548869 PMCID: PMC9425300 DOI: 10.3324/haematol.2021.280455] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Indexed: 11/09/2022] Open
Abstract
Not available.
Collapse
Affiliation(s)
| | | | | | - Emma E Ilett
- PERSIMUNE Centre of Excellence, Rigshospitalet, Copenhagen
| | | | - Marc Noguera-Julian
- Institut de Recerca de la Sida-IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain; University of Vic-Central University of Catalonia, Barcelona
| | - Roger Paredes
- Institut de Recerca de la Sida-IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain; Infectious Diseases Department, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia
| | | | - Carsten U Niemann
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen.
| |
Collapse
|
6
|
Kaur M, MacPherson CR, Schmeier S, Narasimhan K, Choolani M, Bajic VB. In Silico discovery of transcription factors as potential diagnostic biomarkers of ovarian cancer. BMC Syst Biol 2011; 5:144. [PMID: 21923952 PMCID: PMC3184078 DOI: 10.1186/1752-0509-5-144] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Accepted: 09/19/2011] [Indexed: 01/21/2023]
Abstract
BACKGROUND Our study focuses on identifying potential biomarkers for diagnosis and early detection of ovarian cancer (OC) through the study of transcription regulation of genes affected by estrogen hormone. RESULTS The results are based on a set of 323 experimentally validated OC-associated genes compiled from several databases, and their subset controlled by estrogen. For these two gene sets we computationally determined transcription factors (TFs) that putatively regulate transcription initiation. We ranked these TFs based on the number of genes they are likely to control. In this way, we selected 17 top-ranked TFs as potential key regulators and thus possible biomarkers for a set of 323 OC-associated genes. For 77 estrogen controlled genes from this set we identified three unique TFs as potential biomarkers. CONCLUSIONS We introduced a new methodology to identify potential diagnostic biomarkers for OC. This report is the first bioinformatics study that explores multiple transcriptional regulators of OC-associated genes as potential diagnostic biomarkers in connection with estrogen responsiveness. We show that 64% of TF biomarkers identified in our study are validated based on real-time data from microarray expression studies. As an illustration, our method could identify CP2 that in combination with CA125 has been reported to be sensitive in diagnosing ovarian tumors.
Collapse
Affiliation(s)
- Mandeep Kaur
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Cameron R MacPherson
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Sebastian Schmeier
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Kothandaraman Narasimhan
- Centre for Excellence in Genomic Medicine Research, King Abdul Aziz University, PO. Box 80216, Jeddah 21589, Kingdom of Saudi Arabia
| | - Mahesh Choolani
- Diagnostic Biomarker Discovery Laboratory, Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University Health System, 5 Lower Kent Ridge Road, 119074, Singapore
| | - Vladimir B Bajic
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| |
Collapse
|
7
|
Abstract
BACKGROUND MicroRNAs (miRNAs) are short non-coding RNA molecules that act as post-transcriptional regulators and affect the regulation of protein-coding genes. Mostly transcribed by PolII, miRNA genes are regulated at the transcriptional level similarly to protein-coding genes. In this study we focus on human miRNAs. These miRNAs are involved in a variety of pathways and can affect many diseases. Our interest is on possible deregulation of the transcription initiation of the miRNA encoding genes, which is facilitated by variations in the genomic sequence of transcriptional control regions (promoters). METHODOLOGY Our aim is to provide an online resource to facilitate the investigation of the potential effects of single nucleotide polymorphisms (SNPs) on miRNA gene regulation. We analyzed SNPs overlapped with predicted transcription factor binding sites (TFBSs) in promoters of miRNA genes. We also accounted for the creation of novel TFBSs due to polymorphisms not present in the reference genome. The resulting changes in the original TFBSs and potential creation of new TFBSs were incorporated into the Dragon Database of Polymorphic Regulation of miRNA genes (dPORE-miRNA). CONCLUSIONS The dPORE-miRNA database enables researchers to explore potential effects of SNPs on the regulation of miRNAs. dPORE-miRNA can be interrogated with regards to: a/miRNAs (their targets, or involvement in diseases, or biological pathways), b/SNPs, or c/transcription factors. dPORE-miRNA can be accessed at http://cbrc.kaust.edu.sa/dpore and http://apps.sanbi.ac.za/dpore/. Its use is free for academic and non-profit users.
Collapse
Affiliation(s)
- Sebastian Schmeier
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Jeddah, Saudi Arabia
| | | | | | | |
Collapse
|
8
|
Schmeier S, MacPherson CR, Essack M, Kaur M, Schaefer U, Suzuki H, Hayashizaki Y, Bajic VB. Deciphering the transcriptional circuitry of microRNA genes expressed during human monocytic differentiation. BMC Genomics 2009; 10:595. [PMID: 20003307 PMCID: PMC2797535 DOI: 10.1186/1471-2164-10-595] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Accepted: 12/10/2009] [Indexed: 12/19/2022] Open
Abstract
Background Macrophages are immune cells involved in various biological processes including host defence, homeostasis, differentiation, and organogenesis. Disruption of macrophage biology has been linked to increased pathogen infection, inflammation and malignant diseases. Differential gene expression observed in monocytic differentiation is primarily regulated by interacting transcription factors (TFs). Current research suggests that microRNAs (miRNAs) degrade and repress translation of mRNA, but also may target genes involved in differentiation. We focus on getting insights into the transcriptional circuitry regulating miRNA genes expressed during monocytic differentiation. Results We computationally analysed the transcriptional circuitry of miRNA genes during monocytic differentiation using in vitro time-course expression data for TFs and miRNAs. A set of TF→miRNA associations was derived from predicted TF binding sites in promoter regions of miRNA genes. Time-lagged expression correlation analysis was utilised to evaluate the TF→miRNA associations. Our analysis identified 12 TFs that potentially play a central role in regulating miRNAs throughout the differentiation process. Six of these 12 TFs (ATF2, E2F3, HOXA4, NFE2L1, SP3, and YY1) have not previously been described to be important for monocytic differentiation. The remaining six TFs are CEBPB, CREB1, ELK1, NFE2L2, RUNX1, and USF2. For several miRNAs (miR-21, miR-155, miR-424, and miR-17-92), we show how their inferred transcriptional regulation impacts monocytic differentiation. Conclusions The study demonstrates that miRNAs and their transcriptional regulatory control are integral molecular mechanisms during differentiation. Furthermore, it is the first study to decipher on a large-scale, how miRNAs are controlled by TFs during human monocytic differentiation. Subsequently, we have identified 12 candidate key controllers of miRNAs during this differentiation process.
Collapse
Affiliation(s)
- Sebastian Schmeier
- South African National Bioinformatics Institute, University of the Western Cape, Modderdam Road, Bellville, South Africa.
| | | | | | | | | | | | | | | |
Collapse
|
9
|
Thompson CL, Pathak SD, Jeromin A, Ng LL, MacPherson CR, Mortrud MT, Cusick A, Riley ZL, Sunkin SM, Bernard A, Puchalski RB, Gage FH, Jones AR, Bajic VB, Hawrylycz MJ, Lein ES. Genomic Anatomy of the Hippocampus. Neuron 2008; 60:1010-21. [DOI: 10.1016/j.neuron.2008.12.008] [Citation(s) in RCA: 303] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2007] [Revised: 07/03/2008] [Accepted: 12/08/2008] [Indexed: 11/16/2022]
|
10
|
Kaur M, Schmeier S, MacPherson CR, Hofmann O, Hide WA, Taylor S, Willcox N, Bajic VB. Prioritizing genes of potential relevance to diseases affected by sex hormones: an example of myasthenia gravis. BMC Genomics 2008; 9:481. [PMID: 18851734 PMCID: PMC2592250 DOI: 10.1186/1471-2164-9-481] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Accepted: 10/13/2008] [Indexed: 11/17/2022] Open
Abstract
Background About 5% of western populations are afflicted by autoimmune diseases many of which are affected by sex hormones. Autoimmune diseases are complex and involve many genes. Identifying these disease-associated genes contributes to development of more effective therapies. Also, association studies frequently imply genomic regions that contain disease-associated genes but fall short of pinpointing these genes. The identification of disease-associated genes has always been challenging and to date there is no universal and effective method developed. Results We have developed a method to prioritize disease-associated genes for diseases affected strongly by sex hormones. Our method uses various types of information available for the genes, but no information that directly links genes with the disease. It generates a score for each of the considered genes and ranks genes based on that score. We illustrate our method on early-onset myasthenia gravis (MG) using genes potentially controlled by estrogen and localized in a genomic segment (which contains the MHC and surrounding region) strongly associated with MG. Based on the considered genomic segment 283 genes are ranked for their relevance to MG and responsiveness to estrogen. The top three ranked genes, HLA-G, TAP2 and HLA-DRB1, are implicated in autoimmune diseases, while TAP2 is associated with SNPs characteristic for MG. Within the top 35 prioritized genes our method identifies 90% of the 10 already known MG-associated genes from the considered region without using any information that directly links genes to MG. Among the top eight genes we identified HLA-G and TUBB as new candidates. We show that our ab-initio approach outperforms the other methods for prioritizing disease-associated genes. Conclusion We have developed a method to prioritize disease-associated genes under the potential control of sex hormones. We demonstrate the success of this method by prioritizing the genes localized in the MHC and surrounding region and evaluating the role of these genes as potential candidates for estrogen control as well as MG. We show that our method outperforms the other methods. The method has a potential to be adapted to prioritize genes relevant to other diseases.
Collapse
Affiliation(s)
- Mandeep Kaur
- South African National Bioinformatics Institute, University of the Western Cape, Bellville, Republic of South Africa.
| | | | | | | | | | | | | | | |
Collapse
|
11
|
James KK, Hurtubise PE, MacPherson CR, Murphy SG. Human lymphocyte membrane immunoglobulin as a reflection of maturation. J Immunol 1974; 113:698-701. [PMID: 4210888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
12
|
Abstract
An experimental infection was induced in mice by intravenous and intraperitoneal inoculation with Oidiodendron kalrai. The infected mice developed a complex neurological syndrome consisting of hyperirritability, jumping, circling, and ataxia, followed by coma and death or by apparent recovery. Visible lesions accompanied by inflammatory reaction and fungal elements were seen only in kidneys, but organisms were also identified in and isolated from the liver, spleen, lungs, and brain. Cortisone alone or in combination with streptomycin rendered the mice highly susceptible to infection with O. kalrai, and lesions were found in the brains as well as in the kidneys of these mice. Treatment of infected mice with streptomycin alone increased the severity and duration of the neurological syndrome, but such treatment did not increase the mortality rate.
Collapse
|
13
|
MacPherson CR. Bacteriological monitoring of the hospital environment. Am J Med Technol 1966; 32:415-9. [PMID: 5342161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|