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Gitau JK, Macharia RW, Mwangi KW, Ongeso N, Murungi E. Gene co-expression network identifies critical genes, pathways and regulatory motifs mediating the progression of rift valley fever in Bostaurus. Heliyon 2023; 9:e18175. [PMID: 37519716 PMCID: PMC10375796 DOI: 10.1016/j.heliyon.2023.e18175] [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: 08/01/2022] [Revised: 07/04/2023] [Accepted: 07/10/2023] [Indexed: 08/01/2023] Open
Abstract
Rift Valley Fever (RVF) is a mosquito-borne viral disease caused by the Rift Valley Fever Virus. The disease is a zoonosis that largely affects domestic animals, including sheep, goats, and cattle, resulting in severe morbidity and mortality marked by massive storm abortions. To halt human and livestock deaths due to RVF, the development of efficacious vaccines and therapeutics is a compelling and urgent priority. We sought to identify potential key modules (gene clusters), hub genes, and regulatory motifs involved in the pathogenesis of RVF in Bos taurus that are amenable to inhibition. We analyzed 39 Bos taurus RNA-Seq samples using the weighted gene co-expression network analysis (WGCNA) R package and uncovered significantly enriched modules containing genes with potential pivotal roles in RVF progression. Moreover, regulatory motif analysis conducted using the Multiple Expectation Maximization for Motif Elicitation (MEME) suite identified motifs that probably modulate vital biological processes. Gene ontology terms associated with identified motifs were inferred using the GoMo human database. The gene co-expression network constructed in WGCNA using 5000 genes contained seven (7) modules, out of which four were significantly enriched for terms associated with response to viruses, response to interferon-alpha, innate immune response, and viral defense. Additionally, several biological pathways implicated in developmental processes, anatomical structure development, and multicellular organism development were identified. Regulatory motifs analysis identified short, repeated motifs whose function(s) may be amenable to disruption by novel therapeutics. Predicted functions of identified motifs include tissue development, embryonic organ development, and organ morphogenesis. We have identified several hub genes in enriched co-expressed gene modules and regulatory motifs potentially involved in the pathogenesis of RVF in B. taurus that are likely viable targets for disruption by novel therapeutics.
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Affiliation(s)
- John K. Gitau
- University of Nairobi, Biochemistry Department, P.O Box 30197, 00100, Nairobi, Kenya
| | - Rosaline W. Macharia
- University of Nairobi, Biochemistry Department, P.O Box 30197, 00100, Nairobi, Kenya
| | - Kennedy W. Mwangi
- Jomo Kenyatta University of Agriculture and Technology, P.O Box 62000, 00200, Nairobi, Kenya
| | - Nehemiah Ongeso
- University of Nairobi, Biochemistry Department, P.O Box 30197, 00100, Nairobi, Kenya
| | - Edwin Murungi
- Kisii University, Department of Medical Biochemistry, P.O Box 408, 40200, Kisii, Kenya
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Braun RO, Brunner L, Wyler K, Auray G, García-Nicolás O, Python S, Zumkehr B, Gaschen V, Stoffel MH, Collin N, Barnier-Quer C, Bruggmann R, Summerfield A. System immunology-based identification of blood transcriptional modules correlating to antibody responses in sheep. NPJ Vaccines 2018; 3:41. [PMID: 30302283 PMCID: PMC6170373 DOI: 10.1038/s41541-018-0078-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 07/07/2018] [Accepted: 07/31/2018] [Indexed: 12/04/2022] Open
Abstract
Inactivated vaccines lack immunogenicity and therefore require potent adjuvants. To understand the in vivo effects of adjuvants, we used a system immunology-based analysis of ovine blood transcriptional modules (BTMs) to dissect innate immune responses relating to either antibody or haptoglobin levels. Using inactivated foot-and-mouth disease virus as an antigen, we compared non-adjuvanted to liposomal-formulated vaccines complemented or not with TLR4 and TLR7 ligands. Early after vaccination, BTM relating to myeloid cells, innate immune responses, dendritic cells, and antigen presentation correlated positively, whereas BTM relating to T and natural killer cells, as well as cell cycle correlated negatively with antibody responses. Interestingly, similar BTM also correlated with haptoglobin, but in a reversed manner, indicating that acute systemic inflammation is not beneficial for early antibody responses. Analysis of vaccine-dependent BTM modulation showed that liposomal formulations induced similar responses to those correlating to antibody levels. Surprisingly, the addition of the TLR ligands appeared to reduce early immunological perturbations and mediated anti-inflammatory effects, despite promoting antibody responses. When pre-vaccination BTM were analyzed, we found that high vaccine responders expressed higher levels of many BTM relating to cell cycle, antigen-presenting cells, and innate responses as compared with low responders. In conclusion, we have transferred human BTM to sheep and identified early vaccine-induced responses associated with antibody levels or unwanted inflammation in a heterogeneous and small group of animals. Such readouts are applicable to other veterinary species and very useful to identify efficient vaccine adjuvants, their mechanism of action, and factors related to low responders.
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Affiliation(s)
- Roman Othmar Braun
- Institute of Virology and Immunology, Mittelhäusern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
- Vetsuisse Faculty, Department of Infectious Disease and Pathobiology, University of Bern, Länggassstrasse 122, 3001 Bern, Switzerland
| | - Livia Brunner
- Vaccine Formulation Laboratory, Department of Biochemistry, University of Lausanne, Lausanne, Switzerland
| | - Kurt Wyler
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Gaël Auray
- Institute of Virology and Immunology, Mittelhäusern, Switzerland
| | - Obdulio García-Nicolás
- Institute of Virology and Immunology, Mittelhäusern, Switzerland
- Vetsuisse Faculty, Department of Infectious Disease and Pathobiology, University of Bern, Länggassstrasse 122, 3001 Bern, Switzerland
| | - Sylvie Python
- Institute of Virology and Immunology, Mittelhäusern, Switzerland
- Vetsuisse Faculty, Department of Infectious Disease and Pathobiology, University of Bern, Länggassstrasse 122, 3001 Bern, Switzerland
| | - Beatrice Zumkehr
- Institute of Virology and Immunology, Mittelhäusern, Switzerland
| | - Véronique Gaschen
- Division of Veterinary Anatomy, University of Bern, Bern, Switzerland
| | | | - Nicolas Collin
- Vaccine Formulation Laboratory, Department of Biochemistry, University of Lausanne, Lausanne, Switzerland
| | - Christophe Barnier-Quer
- Vaccine Formulation Laboratory, Department of Biochemistry, University of Lausanne, Lausanne, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Artur Summerfield
- Institute of Virology and Immunology, Mittelhäusern, Switzerland
- Vetsuisse Faculty, Department of Infectious Disease and Pathobiology, University of Bern, Länggassstrasse 122, 3001 Bern, Switzerland
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Shakil S, Billings JC, Keilholz SD, Lee CH. Parametric Dependencies of Sliding Window Correlation. IEEE Trans Biomed Eng 2017; 65:254-263. [PMID: 29035206 DOI: 10.1109/tbme.2017.2762763] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVE In this paper, we explore the dependence of sliding window correlation (SWC) results on different parameters of correlating signals. The SWC is extensively used to explore the dynamics of functional connectivity (FC) networks using resting-state functional MRI (rsfMRI) scans. These scanned signals often contain multiple amplitudes, frequencies, and phases. However, the exact values of these parameters are unknown. Two recent studies explored the relationship of window length and frequencies (minimum/maximum) in the correlating signals. METHODS We extend the findings of these studies by using two deterministic signals with multiple amplitudes, frequencies, and phases. Afterward, we modulate one of the signals to introduce dynamics (nonstationarity) in their relationship. We also explore the relationship of window length and frequency band for real rsfMRI data. RESULTS For deterministic signals, the spurious fluctuations due to the method itself minimize, and the SWC estimates the stationary correlation when frequencies in the signals have specific relationship. For dynamic relationship also, the undesirable frequencies were removed under specific conditions for the frequencies. For real rsfMRI data, the SWC results varied with frequencies and window length. CONCLUSION In the absence of any "ground truth" for different parameters in real rsfMRI signals, the SWC with a constant window size may not be a reliable method to study the dynamics of the FC. SIGNIFICANCE This study reveals the parametric dependencies of the SWC and its limitation as a method to analyze dynamics of FC networks in the absence of any ground truth.
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Khare S, Drake KL, Lawhon SD, Nunes JES, Figueiredo JF, Rossetti CA, Gull T, Everts RE, Lewin HA, Adams LG. Systems Analysis of Early Host Gene Expression Provides Clues for Transient Mycobacterium avium ssp avium vs. Persistent Mycobacterium avium ssp paratuberculosis Intestinal Infections. PLoS One 2016; 11:e0161946. [PMID: 27653506 PMCID: PMC5031438 DOI: 10.1371/journal.pone.0161946] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/15/2016] [Indexed: 02/06/2023] Open
Abstract
It has long been a quest in ruminants to understand how two very similar mycobacterial species, Mycobacterium avium ssp. paratuberculosis (MAP) and Mycobacterium avium ssp. avium (MAA) lead to either a chronic persistent infection or a rapid-transient infection, respectively. Here, we hypothesized that when the host immune response is activated by MAP or MAA, the outcome of the infection depends on the early activation of signaling molecules and host temporal gene expression. To test our hypothesis, ligated jejuno-ileal loops including Peyer’s patches in neonatal calves were inoculated with PBS, MAP, or MAA. A temporal analysis of the host transcriptome profile was conducted at several times post-infection (0.5, 1, 2, 4, 8 and 12 hours). When comparing the transcriptional responses of calves infected with the MAA versus MAP, discordant patterns of mucosal expression were clearly evident, and the numbers of unique transcripts altered were moderately less for MAA-infected tissue than were mucosal tissues infected with the MAP. To interpret these complex data, changes in the gene expression were further analyzed by dynamic Bayesian analysis. Bayesian network modeling identified mechanistic genes, gene-to-gene relationships, pathways and Gene Ontologies (GO) biological processes that are involved in specific cell activation during infection. MAP and MAA had significant different pathway perturbation at 0.5 and 12 hours post inoculation. Inverse processes were observed between MAP and MAA response for epithelial cell proliferation, negative regulation of chemotaxis, cell-cell adhesion mediated by integrin and regulation of cytokine-mediated signaling. MAP inoculated tissue had significantly lower expression of phagocytosis receptors such as mannose receptor and complement receptors. This study reveals that perturbation of genes and cellular pathways during MAP infection resulted in host evasion by mucosal membrane barrier weakening to access entry in the ileum, inhibition of Ca signaling associated with decreased phagosome-lysosome fusion as well as phagocytosis inhibition, bias toward Th2 cell immune response accompanied by cell recruitment, cell proliferation and cell differentiation; leading to persistent infection. Contrarily, MAA infection was related to cellular responses associated with activation of molecular pathways that release chemicals and cytokines involved with containment of infection and a strong bias toward Th1 immune response, resulting in a transient infection.
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Affiliation(s)
- Sangeeta Khare
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, 77843, United States of America
- Division of Microbiology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, 72079, United States of America
- * E-mail: (SK); (LGA)
| | | | - Sara D. Lawhon
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, 77843, United States of America
| | - Jairo E. S. Nunes
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, 77843, United States of America
| | - Josely F. Figueiredo
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, 77843, United States of America
| | - Carlos A. Rossetti
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, 77843, United States of America
| | - Tamara Gull
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, 77843, United States of America
| | - Robin E. Everts
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, United States of America
| | - Harris. A. Lewin
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, United States of America
| | - Leslie Garry Adams
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, 77843, United States of America
- * E-mail: (SK); (LGA)
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Laughin RC, Drake KL, Morrill JC, Adams LG. Correction: Correlative Gene Expression to Protective Seroconversion In Rift Valley Vaccinates. PLoS One 2016; 11:e0156469. [PMID: 27214231 PMCID: PMC4877044 DOI: 10.1371/journal.pone.0156469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0147027.].
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