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Wang J, Zhao E, Geng B, Zhang W, Li Z, Liu Q, Liu W, Zhang W, Hou W, Zhang N, Liu Z, You B, Wu P, Li X. Downregulation of UBB potentiates SP1/VEGFA-dependent angiogenesis in clear cell renal cell carcinoma. Oncogene 2024; 43:1386-1396. [PMID: 38467852 PMCID: PMC11065696 DOI: 10.1038/s41388-024-03003-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/13/2024]
Abstract
Clear cell renal cell carcinoma (ccRCC) presents a unique profile characterized by high levels of angiogenesis and robust vascularization. Understanding the underlying mechanisms driving this heterogeneity is essential for developing effective therapeutic strategies. This study revealed that ubiquitin B (UBB) is downregulated in ccRCC, which adversely affects the survival of ccRCC patients. UBB exerts regulatory control over vascular endothelial growth factor A (VEGFA) by directly interacting with specificity protein 1 (SP1), consequently exerting significant influence on angiogenic processes. Subsequently, we validated that DNA methyltransferase 3 alpha (DNMT3A) is located in the promoter of UBB to epigenetically inhibit UBB transcription. Additionally, we found that an unharmonious UBB/VEGFA ratio mediates pazopanib resistance in ccRCC. These findings underscore the critical involvement of UBB in antiangiogenic therapy and unveil a novel therapeutic strategy for ccRCC.
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Affiliation(s)
- Jinpeng Wang
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Enyang Zhao
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Bo Geng
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Wei Zhang
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Zhuolun Li
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Qing Liu
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
- Department of Radiation Oncology, Urology, and Pathology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Weiyang Liu
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Wenfu Zhang
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Wenbin Hou
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Nan Zhang
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China
| | - Zhiming Liu
- Department of Urology, Shanghai Fengxian District Central Hospital, Shanghai, 200233, China
| | - Bosen You
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China.
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China.
| | - Pengfei Wu
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China.
- Anhui Province Key Laboratory of Brain Function and Brain Disease, Hefei, Anhui, 230001, China.
- Anhui Provincial Stereotactic Neurosurgical Institute, Hefei, Anhui, 230001, China.
- Anhui Provincial Clinical Research Center for Neurosurgical Disease, Hefei, Anhui, 230001, China.
- Anhui Province Key Laboratory of Cancer Translational Medicine, Bengbu Medical University, 2600 Donghai Avenue, Bengbu, Anhui, 233030, China.
| | - Xuedong Li
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150086, China.
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Gusareva ES, Lorenzini PA, Ramli NAB, Ghosh AG, Kim HL. Population-specific adaptation in malaria-endemic regions of asia. J Bioinform Comput Biol 2021; 19:2140006. [PMID: 34753405 DOI: 10.1142/s0219720021400060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Evolutionary mechanisms of adaptation to malaria are understudied in Asian endemic regions despite a high prevalence of malaria in the region. In our research, we performed a genome-wide screening for footprints of natural selection against malaria by comparing eight Asian population groups from malaria-endemic regions with two non-endemic population groups from Europe and Mongolia. We identified 285 adaptive genes showing robust selection signals across three statistical methods, iHS, XP-EHH, and PBS. Interestingly, most of the identified genes (82%) were found to be under selection in a single population group, while adaptive genes shared across populations were rare. This is likely due to the independent adaptation history in different endemic populations. The gene ontology (GO) analysis for the 285 adaptive genes highlighted their functional processes linked to neuronal organizations or nervous system development. These genes could be related to cerebral malaria and may reduce the inflammatory response and the severity of malaria symptoms. Remarkably, our novel population genomic approach identified population-specific adaptive genes potentially against malaria infection without the need for patient samples or individual medical records.
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Affiliation(s)
- Elena S Gusareva
- Asian School of the Environment, Nanyang Technological University, Nanyang Dr, 637459 Singapore.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551 Singapore
| | - Paolo Alberto Lorenzini
- Asian School of the Environment, Nanyang Technological University, Nanyang Dr, 637459 Singapore
| | - Nurul Adilah Binte Ramli
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551 Singapore
| | - Amit Gourav Ghosh
- Asian School of the Environment, Nanyang Technological University, Nanyang Dr, 637459 Singapore
| | - Hie Lim Kim
- Asian School of the Environment, Nanyang Technological University, Nanyang Dr, 637459 Singapore.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551 Singapore
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3
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Onaolapo OJ, Onaolapo AY, Olowe OA, Udoh MO, Udoh DO, Nathaniel TI. Melatonin and Melatonergic Influence on Neuronal Transcription Factors: Implications for the Development of Novel Therapies for Neurodegenerative Disorders. Curr Neuropharmacol 2021; 18:563-577. [PMID: 31885352 PMCID: PMC7457420 DOI: 10.2174/1570159x18666191230114339] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/16/2019] [Accepted: 12/28/2019] [Indexed: 01/04/2023] Open
Abstract
Melatonin is a multifunctional signalling molecule that is secreted by the mammalian pineal gland, and also found in a number of organisms including plants and bacteria. Research has continued to uncover an ever-increasing number of processes in which melatonin is known to play crucial roles in mammals. Amongst these functions is its contribution to cell multiplication, differentiation and survival in the brain. Experimental studies show that melatonin can achieve these functions by influencing transcription factors which control neuronal and glial gene expression. Since neuronal survival and differentiation are processes that are important determinants of the pathogenesis, course and outcome of neurodegenerative disorders; the known and potential influences of melatonin on neuronal and glial transcription factors are worthy of constant examination. In this review, relevant scientific literature on the role of melatonin in preventing or altering the course and outcome of neurodegenerative disorders, by focusing on melatonin's influence on transcription factors is examined. A number of transcription factors whose functions can be influenced by melatonin in neurodegenerative disease models have also been highlighted. Finally, the therapeutic implications of melatonin's influences have also been discussed and the potential limitations to its applications have been highlighted.
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Affiliation(s)
- Olakunle J. Onaolapo
- Behavioural Neuroscience/Neuropharmacology Unit, Department of Pharmacology, Ladoke Akintola University of Technology, Osogbo, Osun State, Nigeria
| | - Adejoke Y. Onaolapo
- Behavioural Neuroscience/Neurobiology Unit, Department of Anatomy, Ladoke Akintola University of Technology, Ogbomosho, Oyo State, Nigeria
| | - Olugbenga A. Olowe
- Molecular Bacteriology and Immunology Unit, Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Osogbo, Osun State, Nigeria
| | - Mojisola O. Udoh
- Department of Pathology, University of Benin Teaching Hospital, Benin City, Nigeria
| | - David O. Udoh
- Division of Neurological Surgery, Department of Surgery, University of Benin Teaching Hospital, Benin City, Edo State, Nigeria
| | - Thomas I. Nathaniel
- University of South Carolina School of Medicine-Greenville, Greenville, South Carolina, 29605, United States
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4
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Gezen-Ak D, Alaylıoğlu M, Genç G, Şengül B, Keskin E, Sordu P, Güleç ZEK, Apaydın H, Bayram-Gürel Ç, Ulutin T, Yılmazer S, Ertan S, Dursun E. Altered Transcriptional Profile of Mitochondrial DNA-Encoded OXPHOS Subunits, Mitochondria Quality Control Genes, and Intracellular ATP Levels in Blood Samples of Patients with Parkinson's Disease. J Alzheimers Dis 2021; 74:287-307. [PMID: 32007957 DOI: 10.3233/jad-191164] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Mitochondrial dysfunctions are significant contributors to neurodegeneration. One result or a cause of mitochondrial dysfunction might be the disruption of mtDNA transcription. Limited data indicated an altered expression of mtDNA encoded transcripts in Alzheimer's disease (AD) or Parkinson's disease (PD). The number of mitochondria is high in cells with a high energy demand, such as muscle or nerve cells. AD or PD involves increased risk of cardiomyopathy, suggesting that mitochondrial dysfunction might be systemic. If it is systemic, we should observe it in different cell types. Given that, we wanted to investigate any disruption in the regulation of mtDNA encoded gene expression in addition to PINK1, PARKIN, and ATP levels in peripheral blood samples of PD cases who are affected by a neurodegenerative disorder that is very well known by its mitochondrial aspects. Our results showed for the first time that: 1) age of onset > 50 PD sporadic (PDS) cases: mtDNA transcription and quality control genes were affected; 2) age of onset <50 PDS cases: only mtDNA transcription was affected; and 3) PD cases with familial background: only quality control genes were affected. mtDNA copy number was not a confounder. Intracellular ATP levels of PD case subgroups were significantly higher than those of healthy subjects. We suggest that a systemic dysregulation of transcription of mtDNA or mitochondrial quality control genes might result in the development of a sporadic form of the disease. Additionally, ATP elevation might be an independent compensatory and response mechanism. Hyperactive cells in AD and PD require further investigation.
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Affiliation(s)
- Duygu Gezen-Ak
- Department of Medical Biology, Brain and Neurodegenerative Disorders Research Laboratories, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Merve Alaylıoğlu
- Department of Medical Biology, Brain and Neurodegenerative Disorders Research Laboratories, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Gençer Genç
- Department of Neurology, Şişli Etfal Training and Research Hospital, Istanbul, Turkey
| | - Büşra Şengül
- Department of Medical Biology, Brain and Neurodegenerative Disorders Research Laboratories, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Ebru Keskin
- Department of Medical Biology, Brain and Neurodegenerative Disorders Research Laboratories, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Pelin Sordu
- Department of Medical Biology, Brain and Neurodegenerative Disorders Research Laboratories, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Zeynep Ece Kaya Güleç
- Department of Neurology, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Hülya Apaydın
- Department of Neurology, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Çiğdem Bayram-Gürel
- Department of Medical Biology, Brain and Neurodegenerative Disorders Research Laboratories, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Turgut Ulutin
- Department of Medical Biology, Brain and Neurodegenerative Disorders Research Laboratories, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Selma Yılmazer
- Department of Medical Biology, Faculty of Medicine, Altınbaş University, Istanbul, Turkey
| | - Sibel Ertan
- Department of Neurology, Faculty of Medicine, Koç University, Istanbul, Turkey
| | - Erdinç Dursun
- Department of Medical Biology, Brain and Neurodegenerative Disorders Research Laboratories, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey.,Department of Neuroscience, Institute of Neurological Sciences, Istanbul University-Cerrahpasa, Istanbul, Turkey
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5
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Understanding Human Cerebral Malaria through a Blood Transcriptomic Signature: Evidences for Erythrocyte Alteration, Immune/Inflammatory Dysregulation, and Brain Dysfunction. Mediators Inflamm 2020; 2020:3280689. [PMID: 32801995 PMCID: PMC7327554 DOI: 10.1155/2020/3280689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 05/08/2020] [Indexed: 12/26/2022] Open
Abstract
Background Cerebral malaria (CM), a reversible encephalopathy affecting young children, is a medical emergency requiring rapid clinical assessment and treatment. However, understanding of the genes/proteins and the biological pathways involved in the disease outcome is still limited. Methods We have performed a whole transcriptomic analysis of blood samples from Malian children with CM or uncomplicated malaria (UM). Hierarchical clustering and pathway, network, and upstream regulator analyses were performed to explore differentially expressed genes (DEGs). We validated gene expression for 8 genes using real-time quantitative PCR (RT-qPCR). Plasma levels were measured for IP-10/CXCL10 and IL-18. Results A blood RNA signature including 538 DEGs (∣FC | ≥2.0, adjusted P value ≤ 0.01) allowed to discriminate between CM and UM. Ingenuity Pathway Analysis (IPA) and Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed novel genes and biological pathways related to immune/inflammatory responses, erythrocyte alteration, and neurodegenerative disorders. Gene expressions of CXCL10, IL12RB2, IL18BP, IL2RA, AXIN2, and NET were significantly lower in CM whereas ARG1 and SLC6A9 were higher in CM compared to UM. Plasma protein levels of IP-10/CXCL10 were significantly lower in CM than in UM while levels of IL-18 were higher. Interestingly, among children with CM, those who died from a complication of malaria tended to have higher concentrations of IP-10/CXCL10 and IFN-γ than those who recovered. Conclusions This study identified some new factors and mechanisms that play crucial roles in CM and characterized their respective biological pathways as well as some upstream regulators.
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Nallandhighal S, Park GS, Ho YY, Opoka RO, John CC, Tran TM. Whole-Blood Transcriptional Signatures Composed of Erythropoietic and NRF2-Regulated Genes Differ Between Cerebral Malaria and Severe Malarial Anemia. J Infect Dis 2019; 219:154-164. [PMID: 30060095 DOI: 10.1093/infdis/jiy468] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/24/2018] [Indexed: 02/03/2023] Open
Abstract
Background Among the severe malaria syndromes, severe malarial anemia (SMA) is the most common, whereas cerebral malaria (CM) is the most lethal. However, the mechanisms that lead to CM and SMA are unclear. Methods We compared transcriptomic profiles of whole blood obtained from Ugandan children with acute CM (n = 17) or SMA (n = 17) and community children without Plasmodium falciparum infection (n = 12) and determined the relationships among gene expression, hematological indices, and relevant plasma biomarkers. Results Both CM and SMA demonstrated predominantly upregulated enrichment of dendritic cell activation, inflammatory/Toll-like receptor/chemokines, and monocyte modules, but downregulated enrichment of lymphocyte modules. Nuclear factor, erythroid 2 like 2 (Nrf2)-regulated genes were overexpressed in children with SMA relative to CM, with the highest expression in children with both SMA and sickle cell disease (HbSS), corresponding with elevated plasma heme oxygenase-1 in this group. Erythroid and reticulocyte-specific signatures were markedly decreased in CM relative to SMA despite higher hemoglobin levels and appropriate increases in erythropoietin. Viral sensing/interferon-regulatory factor 2 module expression and plasma interferon-inducible protein-10/CXCL10 negatively correlated with reticulocyte-specific signatures. Conclusions Compared with SMA, CM is associated with downregulation of Nrf2-related and erythropoiesis signatures by whole-blood transcriptomics. Future studies are needed to confirm these findings and assess pathways that may be amenable to interventions to ameliorate CM and SMA.
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Affiliation(s)
- Srinivas Nallandhighal
- Division of Infectious Diseases, Department of Medicine, Indiana University School of Medicine, Indianapolis
| | - Gregory S Park
- Division of Global Pediatrics, Department of Pediatrics, University of Minnesota Medical School, Minneapolis
| | - Yen-Yi Ho
- Department of Statistics, College of Arts and Sciences, University of South Carolina, Columbia
| | - Robert O Opoka
- Department of Paediatrics and Child Health, Makerere University, Kampala, Uganda
| | - Chandy C John
- Division of Infectious Diseases, Department of Medicine, Indiana University School of Medicine, Indianapolis.,Division of Global Pediatrics, Department of Pediatrics, University of Minnesota Medical School, Minneapolis.,Ryan White Center for Pediatric Infectious Disease and Global Health, Indiana University School of Medicine, Indianapolis
| | - Tuan M Tran
- Division of Infectious Diseases, Department of Medicine, Indiana University School of Medicine, Indianapolis.,Ryan White Center for Pediatric Infectious Disease and Global Health, Indiana University School of Medicine, Indianapolis
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7
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Thiam A, Sanka M, Ndiaye Diallo R, Torres M, Mbengue B, Nunez NF, Thiam F, Diop G, Victorero G, Nguyen C, Dieye A, Rihet P. Gene expression profiling in blood from cerebral malaria patients and mild malaria patients living in Senegal. BMC Med Genomics 2019; 12:148. [PMID: 31666081 PMCID: PMC6821028 DOI: 10.1186/s12920-019-0599-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 10/09/2019] [Indexed: 01/06/2023] Open
Abstract
Background Plasmodium falciparum malaria remains a major health problem in Africa. The mechanisms of pathogenesis are not fully understood. Transcriptomic studies may provide new insights into molecular pathways involved in the severe form of the disease. Methods Blood transcriptional levels were assessed in patients with cerebral malaria, non-cerebral malaria, or mild malaria by using microarray technology to look for gene expression profiles associated with clinical status. Multi-way ANOVA was used to extract differentially expressed genes. Network and pathways analyses were used to detect enrichment for biological pathways. Results We identified a set of 443 genes that were differentially expressed in the three patient groups after applying a false discovery rate of 10%. Since the cerebral patients displayed a particular transcriptional pattern, we focused our analysis on the differences between cerebral malaria patients and mild malaria patients. We further found 842 differentially expressed genes after applying a false discovery rate of 10%. Unsupervised hierarchical clustering of cerebral malaria-informative genes led to clustering of the cerebral malaria patients. The support vector machine method allowed us to correctly classify five out of six cerebral malaria patients and six of six mild malaria patients. Furthermore, the products of the differentially expressed genes were mapped onto a human protein-protein network. This led to the identification of the proteins with the highest number of interactions, including GSK3B, RELA, and APP. The enrichment analysis of the gene functional annotation indicates that genes involved in immune signalling pathways play a role in the occurrence of cerebral malaria. These include BCR-, TCR-, TLR-, cytokine-, FcεRI-, and FCGR- signalling pathways and natural killer cell cytotoxicity pathways, which are involved in the activation of immune cells. In addition, our results revealed an enrichment of genes involved in Alzheimer’s disease. Conclusions In the present study, we examine a set of genes whose expression differed in cerebral malaria patients and mild malaria patients. Moreover, our results provide new insights into the potential effect of the dysregulation of gene expression in immune pathways. Host genetic variation may partly explain such alteration of gene expression. Further studies are required to investigate this in African populations.
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Affiliation(s)
- Alassane Thiam
- Unité d'Immunogénétique, Institut Pasteur de Dakar, Dakar, Sénégal
| | - Michel Sanka
- Aix Marseille Univ, INSERM, TAGC UMR U1090, 163 Av de Luminy, 13288, Marseille, cedex 9, France
| | - Rokhaya Ndiaye Diallo
- Service de Génétique Humaine, Faculté de Médecine, de Pharmacie et d'Odontostomatologie, UCAD, Dakar, Sénégal
| | - Magali Torres
- Aix Marseille Univ, INSERM, TAGC UMR U1090, 163 Av de Luminy, 13288, Marseille, cedex 9, France
| | - Babacar Mbengue
- Service Immunologie, Faculte de Medecine, Université Cheikh Anta Diop de Dakar, Dakar, Sénégal
| | - Nicolas Fernandez Nunez
- Aix Marseille Univ, INSERM, TAGC UMR U1090, 163 Av de Luminy, 13288, Marseille, cedex 9, France
| | - Fatou Thiam
- Département de Génie chimique et biologie, Ecole Supérieure Polytechnique, Université Cheikh Anta Diop de Dakar, Dakar, Sénégal
| | - Gora Diop
- Unité d'Immunogénétique, Institut Pasteur de Dakar, Dakar, Sénégal.,Département de Biologie animale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop de Dakar, Dakar, Sénégal
| | - Geneviève Victorero
- Aix Marseille Univ, INSERM, TAGC UMR U1090, 163 Av de Luminy, 13288, Marseille, cedex 9, France
| | - Catherine Nguyen
- Aix Marseille Univ, INSERM, TAGC UMR U1090, 163 Av de Luminy, 13288, Marseille, cedex 9, France
| | - Alioune Dieye
- Unité d'Immunogénétique, Institut Pasteur de Dakar, Dakar, Sénégal.,Service Immunologie, Faculte de Medecine, Université Cheikh Anta Diop de Dakar, Dakar, Sénégal
| | - Pascal Rihet
- Aix Marseille Univ, INSERM, TAGC UMR U1090, 163 Av de Luminy, 13288, Marseille, cedex 9, France.
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8
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Loiseau C, Cooper MM, Doolan DL. Deciphering host immunity to malaria using systems immunology. Immunol Rev 2019; 293:115-143. [PMID: 31608461 DOI: 10.1111/imr.12814] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 12/11/2022]
Abstract
A century of conceptual and technological advances in infectious disease research has changed the face of medicine. However, there remains a lack of effective interventions and a poor understanding of host immunity to the most significant and complex pathogens, including malaria. The development of successful interventions against such intractable diseases requires a comprehensive understanding of host-pathogen immune responses. A major advance of the past decade has been a paradigm switch in thinking from the contemporary reductionist (gene-by-gene or protein-by-protein) view to a more holistic (whole organism) view. Also, a recognition that host-pathogen immunity is composed of complex, dynamic interactions of cellular and molecular components and networks that cannot be represented by any individual component in isolation. Systems immunology integrates the field of immunology with omics technologies and computational sciences to comprehensively interrogate the immune response at a systems level. Herein, we describe the system immunology toolkit and report recent studies deploying systems-level approaches in the context of natural exposure to malaria or controlled human malaria infection. We contribute our perspective on the potential of systems immunity for the rational design and development of effective interventions to improve global public health.
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Affiliation(s)
- Claire Loiseau
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Qld, Australia
| | - Martha M Cooper
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Qld, Australia
| | - Denise L Doolan
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Qld, Australia
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9
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Lee HJ, Georgiadou A, Otto TD, Levin M, Coin LJ, Conway DJ, Cunnington AJ. Transcriptomic Studies of Malaria: a Paradigm for Investigation of Systemic Host-Pathogen Interactions. Microbiol Mol Biol Rev 2018; 82:e00071-17. [PMID: 29695497 PMCID: PMC5968457 DOI: 10.1128/mmbr.00071-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Transcriptomics, the analysis of genome-wide RNA expression, is a common approach to investigate host and pathogen processes in infectious diseases. Technical and bioinformatic advances have permitted increasingly thorough analyses of the association of RNA expression with fundamental biology, immunity, pathogenesis, diagnosis, and prognosis. Transcriptomic approaches can now be used to realize a previously unattainable goal, the simultaneous study of RNA expression in host and pathogen, in order to better understand their interactions. This exciting prospect is not without challenges, especially as focus moves from interactions in vitro under tightly controlled conditions to tissue- and systems-level interactions in animal models and natural and experimental infections in humans. Here we review the contribution of transcriptomic studies to the understanding of malaria, a parasitic disease which has exerted a major influence on human evolution and continues to cause a huge global burden of disease. We consider malaria a paradigm for the transcriptomic assessment of systemic host-pathogen interactions in humans, because much of the direct host-pathogen interaction occurs within the blood, a readily sampled compartment of the body. We illustrate lessons learned from transcriptomic studies of malaria and how these lessons may guide studies of host-pathogen interactions in other infectious diseases. We propose that the potential of transcriptomic studies to improve the understanding of malaria as a disease remains partly untapped because of limitations in study design rather than as a consequence of technological constraints. Further advances will require the integration of transcriptomic data with analytical approaches from other scientific disciplines, including epidemiology and mathematical modeling.
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Affiliation(s)
- Hyun Jae Lee
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | | | - Thomas D Otto
- Centre of Immunobiology, University of Glasgow, Glasgow, United Kingdom
| | - Michael Levin
- Section of Paediatrics, Imperial College, London, United Kingdom
| | - Lachlan J Coin
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - David J Conway
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
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10
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Smith ML, Styczynski MP. Systems Biology-Based Investigation of Host-Plasmodium Interactions. Trends Parasitol 2018; 34:617-632. [PMID: 29779985 DOI: 10.1016/j.pt.2018.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 04/10/2018] [Accepted: 04/16/2018] [Indexed: 12/20/2022]
Abstract
Malaria is a serious, complex disease caused by parasites of the genus Plasmodium. Plasmodium parasites affect multiple tissues as they evade immune responses, replicate, sexually reproduce, and transmit between vertebrate and invertebrate hosts. The explosion of omics technologies has enabled large-scale collection of Plasmodium infection data, revealing systems-scale patterns, mechanisms of pathogenesis, and the ways that host and pathogen affect each other. Here, we provide an overview of recent efforts using systems biology approaches to study host-Plasmodium interactions and the biological themes that have emerged from these efforts. We discuss some of the challenges in using systems biology for this goal, key research efforts needed to address those issues, and promising future malaria applications of systems biology.
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Affiliation(s)
- Maren L Smith
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; Malaria Host-Pathogen Interaction Center, Emory University, Atlanta, GA 30322, USA
| | - Mark P Styczynski
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; Malaria Host-Pathogen Interaction Center, Emory University, Atlanta, GA 30322, USA.
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