1
|
Yadav AK, Singh TR. Computational approach for assessing the involvement of SMYD2 protein in human cancers using TCGA data. J Genet Eng Biotechnol 2023; 21:122. [PMID: 37971632 PMCID: PMC10654300 DOI: 10.1186/s43141-023-00594-7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 11/06/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND SMYD2 is a protein of the SET and MYND domain-containing family SMYD. It can methylate the lysine residue of various histone and nonhistone cancer-related proteins and plays a critical role in tumorigenesis. Although emerging evidence supports the association of SMYD2 in the progression of cancers, but its definitive effect is not yet clear. Therefore, further study of the gene in relation with cancer progression needs to be conducted. In the current study, investigators used TCGA data to determine the potential carcinogenic effect of SMYD2 in 11 cancer types. The transcriptional expression, survival rate, mutations, enriched pathways, and Gene Ontology of the SMYD2 were explored using different bioinformatics tools and servers. In addition, we also examined the correlation between SMYD2 gene expression and immunocyte infiltration in multiple cancer types. RESULTS Findings revealed that higher expression of SMYD2 was significantly correlated with cancer incidents. In CESC and KIRC, the mRNA expression of SMYD2 was significantly correlated with overall survival (OS). In BRCA, KIRC, COAD, and HNSC, the mRNA expression of SMYD2 was significantly correlated with disease-free survival (DFS). We detected 15 missense, 4 truncating, 4 fusions, and 1 splice type of mutation. The expression of SMYD2 was significantly correlated with tumor purity and immunocyte infiltration in six cancer types. The gene GNPAT was highly associated with SMYD2. Significant pathways and Gene Ontology (GO) terms for co-expressed genes were associated to various processes linked with cancer formation. CONCLUSION Collectively, our data-driven results may provide reasonably comprehensive insights for understanding the carcinogenic effect of SMYD2. It suggests that SMYD2 might be used as a significant target for identifying new biomarkers for various human tumors.
Collapse
Affiliation(s)
- Arvind Kumar Yadav
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan-173234, Himachal Pradesh, India
| | - Tiratha Raj Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan-173234, Himachal Pradesh, India.
- Centre of Excellence in Healthcare Technologies and Informatics (CHETI), Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan-173234, Himachal Pradesh, India.
| |
Collapse
|
2
|
Gómez-Carballa A, Rivero-Calle I, Pardo-Seco J, Gómez-Rial J, Rivero-Velasco C, Rodríguez-Núñez N, Barbeito-Castiñeiras G, Pérez-Freixo H, Cebey-López M, Barral-Arca R, Rodriguez-Tenreiro C, Dacosta-Urbieta A, Bello X, Pischedda S, Currás-Tuala MJ, Viz-Lasheras S, Martinón-Torres F, Salas A. A multi-tissue study of immune gene expression profiling highlights the key role of the nasal epithelium in COVID-19 severity. Environ Res 2022; 210:112890. [PMID: 35202626 PMCID: PMC8861187 DOI: 10.1016/j.envres.2022.112890] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/11/2022] [Accepted: 02/02/2022] [Indexed: 05/08/2023]
Abstract
Coronavirus Disease-19 (COVID-19) symptoms range from mild to severe illness; the cause for this differential response to infection remains unknown. Unravelling the immune mechanisms acting at different levels of the colonization process might be key to understand these differences. We carried out a multi-tissue (nasal, buccal and blood; n = 156) gene expression analysis of immune-related genes from patients affected by different COVID-19 severities, and healthy controls through the nCounter technology. Mild and asymptomatic cases showed a powerful innate antiviral response in nasal epithelium, characterized by activation of interferon (IFN) pathway and downstream cascades, successfully controlling the infection at local level. In contrast, weak macrophage/monocyte driven innate antiviral response and lack of IFN signalling activity were present in severe cases. Consequently, oral mucosa from severe patients showed signals of viral activity, cell arresting and viral dissemination to the lower respiratory tract, which ultimately could explain the exacerbated innate immune response and impaired adaptative immune responses observed at systemic level. Results from saliva transcriptome suggest that the buccal cavity might play a key role in SARS-CoV-2 infection and dissemination in patients with worse prognosis. Co-expression network analysis adds further support to these findings, by detecting modules specifically correlated with severity involved in the abovementioned biological routes; this analysis also provides new candidate genes that might be tested as biomarkers in future studies. We also found tissue specific severity-related signatures mainly represented by genes involved in the innate immune system and cytokine/chemokine signalling. Local immune response could be key to determine the course of the systemic response and thus COVID-19 severity. Our findings provide a framework to investigate severity host gene biomarkers and pathways that might be relevant to diagnosis, prognosis, and therapy.
Collapse
Affiliation(s)
- Alberto Gómez-Carballa
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Irene Rivero-Calle
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain; Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jacobo Pardo-Seco
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - José Gómez-Rial
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain; Laboratorio de Inmunología. Servicio de Análisis Clínicos. Hospital Clínico Universitario (SERGAS), Galicia, Spain
| | - Carmen Rivero-Velasco
- Intensive Medicine Department, Hospital Clìnico Universitario de Santiago de Compostela, Galicia, Spain
| | - Nuria Rodríguez-Núñez
- Pneumology Department, Hospital Clìnico Universitario de Santiago de Compostela, Galicia, Spain
| | - Gema Barbeito-Castiñeiras
- Clinical Microbiology Unit, Complexo Hospitalario Universitario de Santiago Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
| | - Hugo Pérez-Freixo
- Preventive Medicine Department, Hospital Clínico Universitario de Santiago de Compostela, Spain
| | - Miriam Cebey-López
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Ruth Barral-Arca
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Carmen Rodriguez-Tenreiro
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain; Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Ana Dacosta-Urbieta
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain; Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Xabier Bello
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Sara Pischedda
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - María José Currás-Tuala
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Sandra Viz-Lasheras
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Federico Martinón-Torres
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain; Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Antonio Salas
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria (IDIS) de Santiago, Santiago de Compostela, Spain; Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela (USC), and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain.
| |
Collapse
|
3
|
Rafi JH, Jafar T, Pathan MT, Reza R, Islam S, Sourna IJ, Alam R, Samad A, Ahammad F. High expression of bone morphogenetic protein 1 (BMP1) is associated with a poor survival rate in human gastric cancer, a dataset approaches. Genomics 2021; 113:1141-54. [PMID: 33189777 DOI: 10.1016/j.ygeno.2020.11.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 11/08/2020] [Accepted: 11/11/2020] [Indexed: 12/21/2022]
Abstract
Bone morphogenetic protein 1 (BMP1) is a secreted metalloprotease of the astacin M12A family of bone morphogenetic proteins (BMPs). BMP1 activates transforming growth factor-β (TGF-β) and BMP signaling pathways by proteolytic cleavage, which has dual roles in gastrointestinal tumor development and progression.TGF-β promotes invasion and metastasis of gastric cancer (GC) by the help of BMP1, so upregulation of the BMP1 may increase cancer invasiveness in GC. In this study,the transcriptional expression, mutations, survival rate, TFs, miRNAs, gene ontology, and signaling pathways of BMP1 were analyzed by using different web servers. We found higher transcriptional and clinicopathological characteristics expression compared to normal tissues, worsening survival rate in GC. We detected 25 missenses, 15 truncating mutations, 23 TFs, and 8 miRNAs. Finally, we identified and analyzed the co-expressed genes and found that the leukemia inhibitory factor is the most positively correlated gene. The gene ontological features and signaling pathways involved in GC development were evaluated as well. We believe that this study will provide a basis for BMP1 to be a significant biomarker for human GC prognosis.
Collapse
|
4
|
Boccarelli A, Esposito F, Coluccia M, Frassanito MA, Vacca A, Del Buono N. Improving knowledge on the activation of bone marrow fibroblasts in MGUS and MM disease through the automatic extraction of genes via a nonnegative matrix factorization approach on gene expression profiles. J Transl Med 2018; 16:217. [PMID: 30075788 DOI: 10.1186/s12967-018-1589-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 07/24/2018] [Indexed: 11/24/2022] Open
Abstract
Background Multiple myeloma (MM) is a cancer of terminally differentiated plasma that is part of a spectrum of blood diseases. The role of the micro-environment is crucial for MM clonal evolution. Methods This paper describes the analysis carried out on a limited number of genes automatically extracted by a nonnegative matrix factorization (NMF) based approach from gene expression profiles of bone marrow fibroblasts of patients with monoclonal gammopathy of undetermined significance (MGUS) and MM. Results Automatic exploration through NMF, combined with a motivated post-processing procedure and a pathways analysis of extracted genes, allowed to infer that a functional switch is required to lead fibroblasts to acquire pro-tumorigenic activity in the progression of the disease from MGUS to MM. Conclusion The extracted biologically relevant genes may be representative of the considered clinical conditions and may contribute to a deeper understanding of tumor behavior. Electronic supplementary material The online version of this article (10.1186/s12967-018-1589-1) contains supplementary material, which is available to authorized users.
Collapse
|
5
|
Susta L, He Y, Hutcheson JM, Lu Y, West FD, Stice SL, Yu P, Abdo Z, Afonso CL. Derivation of chicken induced pluripotent stem cells tolerant to Newcastle disease virus-induced lysis through multiple rounds of infection. Virol J 2016; 13:205. [PMID: 27919263 PMCID: PMC5139146 DOI: 10.1186/s12985-016-0659-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 11/25/2016] [Indexed: 12/29/2022] Open
Abstract
Background Newcastle disease (ND), caused by Newcastle disease virus (NDV), is a devastating disease of poultry and wild birds. ND is prevented by rigorous biocontainment and vaccination. One potential approach to prevent spread of the virus is production of birds that show innate resistance to NDV-caused disease. Induced pluripotent stem cell (iPSC) technology allows adult cells to be reprogrammed into an embryonic stem cell-like state capable of contributing to live offspring and passing on unique traits in a number of species. Recently, iPSC approaches have been successfully applied to avian cells. If chicken induced pluripotent stem cells (ciPSCs) are genetically or epigenetically modified to resist NDV infection, it may be possible to generate ND resistant poultry. There is limited information on the potential of ciPSCs to be infected by NDV, or the capacity of these cells to become resistant to infection. The aim of the present work was to assess the characteristics of the interaction between NDV and ciPSCs, and to develop a selection method that would increase tolerance of these cells to NDV-induced cellular damage. Results Results showed that ciPSCs were permissive to infection with NDV, and susceptible to virus-mediated cell death. Since ciPSCs that survived infection demonstrated the ability to recover quickly, we devised a system to select surviving cells through multiple infection rounds with NDV. ciPSCs that sustained 9 consecutive infections had a statistically significant increase in survival (up to 36 times) compared to never-infected ciPSCs upon NDV infection (tolerant cells). Increased survival was not caused by a loss of permissiveness to NDV replication. RNA sequencing followed by enrichment pathway analysis showed that numerous metabolic pathways where differentially regulated between tolerant and never-infected ciPSCs. Conclusions Results demonstrate that ciPSCs are permissive to NDV infection and become increasingly tolerant to NDV under selective pressure, indicating that this system could be applied to study mechanisms of cellular tolerance to NDV. Electronic supplementary material The online version of this article (doi:10.1186/s12985-016-0659-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Leonardo Susta
- US National Poultry Research Center, Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, Athens, GA, 30605, USA. .,Present address: Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, N1G 2 W1, Canada.
| | - Ying He
- Regenerative Bioscience Center, University of Georgia, Athens, GA, 30602, USA.,Present address: College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, 53004, China
| | - Jessica M Hutcheson
- Regenerative Bioscience Center, University of Georgia, Athens, GA, 30602, USA.,Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA
| | - Yangqing Lu
- Regenerative Bioscience Center, University of Georgia, Athens, GA, 30602, USA.,Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA
| | - Franklin D West
- Regenerative Bioscience Center, University of Georgia, Athens, GA, 30602, USA.,Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA
| | - Steven L Stice
- Regenerative Bioscience Center, University of Georgia, Athens, GA, 30602, USA.,Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA
| | - Ping Yu
- Regenerative Bioscience Center, University of Georgia, Athens, GA, 30602, USA.,Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA
| | - Zaid Abdo
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Claudio L Afonso
- US National Poultry Research Center, Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, Athens, GA, 30605, USA
| |
Collapse
|
6
|
Abramsky T, Devries KM, Michau L, Nakuti J, Musuya T, Kiss L, Kyegombe N, Watts C. Ecological pathways to prevention: How does the SASA! community mobilisation model work to prevent physical intimate partner violence against women? BMC Public Health 2016; 16:339. [PMID: 27084116 PMCID: PMC4833941 DOI: 10.1186/s12889-016-3018-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 04/08/2016] [Indexed: 11/29/2022] Open
Abstract
Background Intimate partner violence (IPV) against women is a global public health concern. While community-level gender norms and attitudes to IPV are recognised drivers of IPV risk, there is little evidence on how interventions might tackle these drivers to prevent IPV at the community-level. This secondary analysis of data from the SASA! study explores the pathways through which SASA!, a community mobilisation intervention to prevent violence against women, achieved community-wide reductions in physical IPV. Methods From 2007 to 2012 a cluster randomised controlled trial (CRT) was conducted in eight communities in Kampala, Uganda. Cross-sectional surveys of a random sample of community members, aged 18–49, were undertaken at baseline (n = 1583) and 4 years post intervention implementation (n = 2532). We used cluster-level intention to treat analysis to estimate SASA!’s community-level impact on women’s past year experience of physical IPV and men’s past year perpetration of IPV. The mediating roles of community-, relationship- and individual-level factors in intervention effect on past year physical IPV experience (women)/perpetration (men) were explored using modified Poisson regression models. Results SASA! was associated with reductions in women’s past year experience of physical IPV (0.48, 95 % CI 0.16–1.39), as well as men’s perpetration of IPV (0.39, 95 % CI 0.20–0.73). Community-level normative attitudes were the most important mediators of intervention impact on physical IPV risk, with norms around the acceptability of IPV explaining 70 % of the intervention effect on women’s experience of IPV and 95 % of the effect on men’s perpetration. The strongest relationship-level mediators were men’s reduced suspicion of partner infidelity (explaining 22 % of effect on men’s perpetration), and improved communication around sex (explaining 16 % of effect on women’s experience). Reduced acceptability of IPV among men was the most important individual-level mediator (explaining 42 % of effect on men’s perpetration). Conclusions These results highlight the important role of community-level norm-change in achieving community-wide reductions in IPV risk. They lend strong support for the more widespread adoption of community-level approaches to preventing violence. Trial registration ClinicalTrials.gov, NCT00790959. Registered 13th November 2008. The study protocol is available at: http://www.trialsjournal.com/content/13/1/96 Electronic supplementary material The online version of this article (doi:10.1186/s12889-016-3018-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Tanya Abramsky
- Gender Violence and Health Centre, London School of Hygiene and Tropical Medicine, 15-17 Tavistock Place, London, WC1H 9SH, UK.
| | - Karen M Devries
- Gender Violence and Health Centre, London School of Hygiene and Tropical Medicine, 15-17 Tavistock Place, London, WC1H 9SH, UK
| | - Lori Michau
- Raising Voices, 16 Tufnell Drive, Kamwokya, P.O Box 6770, Kampala, Uganda
| | - Janet Nakuti
- Raising Voices, 16 Tufnell Drive, Kamwokya, P.O Box 6770, Kampala, Uganda
| | - Tina Musuya
- Centre for Domestic Violence Prevention, 16 Tufnell Drive, Kamwokya, P.O Box 6770, Kampala, Uganda
| | - Ligia Kiss
- Gender Violence and Health Centre, London School of Hygiene and Tropical Medicine, 15-17 Tavistock Place, London, WC1H 9SH, UK
| | - Nambusi Kyegombe
- Gender Violence and Health Centre, London School of Hygiene and Tropical Medicine, 15-17 Tavistock Place, London, WC1H 9SH, UK
| | - Charlotte Watts
- Gender Violence and Health Centre, London School of Hygiene and Tropical Medicine, 15-17 Tavistock Place, London, WC1H 9SH, UK
| |
Collapse
|
7
|
Wang W, Mohsen AW, Uechi G, Schreiber E, Balasubramani M, Day B, Michael Barmada M, Vockley J. Complex changes in the liver mitochondrial proteome of short chain acyl-CoA dehydrogenase deficient mice. Mol Genet Metab 2014; 112:30-9. [PMID: 24685553 PMCID: PMC4167795 DOI: 10.1016/j.ymgme.2014.02.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 02/18/2014] [Accepted: 02/19/2014] [Indexed: 10/25/2022]
Abstract
Short-chain acyl-CoA dehydrogenase (SCAD) deficiency is an autosomal recessive inborn error of metabolism that leads to the impaired mitochondrial fatty acid β-oxidation of short chain fatty acids. It is heterogeneous in clinical presentation including asymptomatic in most patients identified by newborn screening. Multiple mutations have been identified in patients; however, neither clear genotype-phenotype relationships nor a good correlation between genotype and current biochemical markers for diagnosis has been identified. The definition and pathophysiology of this deficiency remain unclear. To better understand this disorder at a global level, quantitative alterations in the mitochondrial proteome in SCAD deficient mice were examined using a combined proteomics approach: two-dimensional gel difference electrophoresis (2DIGE) followed by protein identification with MALDI-TOF/TOF and iTRAQ labeling followed by nano-LC/MALDI-TOF/TOF. We found broad mitochondrial dysfunction in SCAD deficiency. Changes in the levels of multiple energy metabolism related proteins were identified indicating that a more complex mechanism for development of symptoms may exist. Affected pathways converge on disorders with neurologic symptoms, suggesting that even asymptomatic individuals with SCAD deficiency may be at risk to develop more severe disease. Our results also identified a pattern associated with hepatotoxicity implicated in mitochondrial dysfunction, fatty acid metabolism, decrease of depolarization of mitochondria and mitochondrial membranes, and swelling of mitochondria, demonstrating that SCAD deficiency relates more directly to mitochondrial dysfunction and alteration of fatty acid metabolism. We propose several candidate molecules that may serve as markers for recognition of clinical risk associated with this disorder.
Collapse
Affiliation(s)
- Wei Wang
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiaotong University, Shanghai, China; Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, USA.
| | - Al-Walid Mohsen
- Division of Medical Genetics, Children's Hospital of Pittsburgh, Pittsburgh, USA
| | - Guy Uechi
- Genomics and Proteomics Core laboratories, University of Pittsburgh, Pittsburgh, USA
| | - Emanuel Schreiber
- Genomics and Proteomics Core laboratories, University of Pittsburgh, Pittsburgh, USA
| | | | - Billy Day
- Genomics and Proteomics Core laboratories, University of Pittsburgh, Pittsburgh, USA
| | - M Michael Barmada
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, USA
| | - Jerry Vockley
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, USA; Division of Medical Genetics, Children's Hospital of Pittsburgh, Pittsburgh, USA; Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, USA
| |
Collapse
|
8
|
Richens JL, Morgan K, O'Shea P. Reverse engineering of Alzheimer's disease based on biomarker pathways analysis. Neurobiol Aging 2014; 35:2029-38. [PMID: 24684789 DOI: 10.1016/j.neurobiolaging.2014.02.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 02/18/2014] [Accepted: 02/26/2014] [Indexed: 12/14/2022]
Abstract
Alzheimer's disease (AD) poses an increasingly profound problem to society, yet progress toward a genuine understanding of the disease remains worryingly slow. Perhaps, the most outstanding problem with the biology of AD is the question of its mechanistic origins, that is, it remains unclear wherein the molecular failures occur that underlie the disease. We demonstrate how molecular biomarkers could help define the nature of AD in terms of the early biochemical events that correlate with disease progression. We use a novel panel of biomolecules that appears in cerebrospinal fluid of AD patients. As changes in the relative abundance of these molecular markers are associated with progression to AD from mild cognitive impairment, we make the assumption that by tracking their origins we can identify the biochemical conditions that predispose their presence and consequently cause the onset of AD. We couple these protein markers with an analysis of a series of genetic factors and together this hypothesis essentially allows us to redefine AD in terms of the molecular pathways that underlie the disease.
Collapse
Affiliation(s)
- Joanna L Richens
- Cell Biophysics Group, School of Life Sciences, Faculty of Medicine & Health Sciences, University Park, University of Nottingham, Nottingham, UK
| | - Kevin Morgan
- Humans Genetics Research Group, School of Life Sciences, Faculty of Medicine & Health Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - Paul O'Shea
- Cell Biophysics Group, School of Life Sciences, Faculty of Medicine & Health Sciences, University Park, University of Nottingham, Nottingham, UK.
| |
Collapse
|