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Wang Z, Liu T, Wang Z, Mi Z, Zhang Y, Wang C, Sun L, Ma S, Xue X, Liu H, Zhang F. CYBB-Mediated Ferroptosis Associated with Immunosuppression in Mycobacterium leprae-Infected Monocyte-Derived Macrophages. J Invest Dermatol 2024; 144:874-887.e2. [PMID: 37925067 DOI: 10.1016/j.jid.2023.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 11/06/2023]
Abstract
Mycobacterium leprae-infected macrophages preferentially exhibit the regulatory M2 phenotype in vitro, which helps the immune escape unabated growth of M leprae in host cells. The mechanism that triggers macrophage polarization is still unknown. In this study, we performed single-cell RNA sequencing to determine the initial responses of human monocyte-derived macrophages against M leprae infection of 4 healthy individuals and found an increase in a major alternative-activated macrophage type that overexpressed NEAT1, CCL2, and CD163. Importantly, further functional analysis showed that ferroptosis was positively correlated with M2 polarization of macrophages, and in vitro experiments have shown that inhibition of ferroptosis promotes the survival of M leprae within macrophages. In addition, further joint analysis of our results with mutisequencing data from patients with leprosy and in vitro validation identified that CYBB was the pivotal molecule for ferroptosis that could promote the M2 polarization of M leprae-infected macrophages, resulting in the immune escape and unabated growth of pathogenic bacteria. Overall, our results suggest that M leprae facilitated its survival by inducing CYBB-mediated macrophage ferroptosis leading to its alternative activation and might reveal the potential for a new therapeutic strategy of leprosy.
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Affiliation(s)
- Zhe Wang
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Tingting Liu
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Zhenzhen Wang
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Zihao Mi
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Yuan Zhang
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Chuan Wang
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Lele Sun
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Shanshan Ma
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Xiaotong Xue
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Hong Liu
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China.
| | - Furen Zhang
- Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China.
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Li Z, Chen H, Feng X, Ruan Y, Yang M. Hematopoietic stem cell transplantation for CYBB heterozygous mutation resulting in very early onset inflammatory bowel disease in children: a case report. BMC Pediatr 2023; 23:348. [PMID: 37434114 DOI: 10.1186/s12887-023-04158-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/25/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND Inflammatory bowel disease (IBD) is a heterogeneous group of disorders associated with environmental triggers and dysregulated immune responses resulting in chronic, recurrent intestinal inflammation. Very early-onset IBD (VEO-IBD) refers to patients with symptoms or diagnosis before the age of 6 years and is widely thought to be associated with monogenic mutations. Traditional drug therapy is often ineffective in this patient population, while hematopoietic stem cell transplantation (HSCT) represents the definitive cure for patients with gene mutations. CASE PRESENTATION We report a case of VEO-IBD associated with a monogenic mutation in a 2-year-old girl presenting mainly with gastrointestinal symptoms, including recurrent hematochezia and abdominal pain for more than 3 months. A gastroscopy revealed erosive gastritis and bulbar duodenitis, while a colonoscopy indicated erosive colitis. Abnormal results were obtained from the dihydrohodamine (DHR) assay and immunoglobulin testing. Whole-exome sequencing identified a heterozygous and de novo nonsense mutation (c.388 C > T; p.R130X) in the CYBB gene leading to deficiency of nicotinamide adenine dinucleotide phosphate (NADPH) oxidase 2 (NOX2) (encoded by CYBB), a critical component of phagocytes. HSCT was performed successfully, and the DHR assay showed that normal neutrophil function was restored. Six months after HSCT, clinical remission was observed, and a repeat colonoscopy revealed intestinal mucosal healing was attained. CONCLUSIONS Patients with CYBB mutations often develop recurrent or severe bacterial or fungal infections, mostly in the lungs, skin, lymph nodes, and liver. Here, we report on a young female child with CYBB mutations presenting predominantly with gastrointestinal symptoms. This study explores the mechanisms of inflammatory bowel disease caused by a monogenic mutation in CYBB to improve early diagnosis and effective treatment rates of this patient population.
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Affiliation(s)
- Zhiling Li
- Department of Pediatrics, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Huan Chen
- Department of Pediatrics, Guangzhou Women And Children's Medical Center, National Children's Medical Center For South Central Region, Guangzhou, Guangdong, China
| | - Xiaoqin Feng
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yongsheng Ruan
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Min Yang
- Department of Pediatrics, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China.
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Ma S, Peng P, Duan Z, Fan Y, Li X. Predicting the Progress of Tuberculosis by Inflammatory Response-Related Genes Based on Multiple Machine Learning Comprehensive Analysis. J Immunol Res 2023; 2023:7829286. [PMID: 37228444 PMCID: PMC10205410 DOI: 10.1155/2023/7829286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/04/2023] [Accepted: 04/20/2023] [Indexed: 05/27/2023] Open
Abstract
Background Tuberculosis (TB), caused by the bacterium Mycobacterium tuberculosis, affects approximately one-quarter of the global population and is considered one of the most lethal infectious diseases worldwide. The prevention of latent tuberculosis infection (LTBI) from progressing into active tuberculosis (ATB) is crucial for controlling and eradicating TB. Unfortunately, currently available biomarkers have limited effectiveness in identifying subpopulations that are at risk of developing ATB. Hence, it is imperative to develop advanced molecular tools for TB risk stratification. Methods The TB datasets were downloaded from the GEO database. Three machine learning models, namely LASSO, RF, and SVM-RFE, were used to identify the key characteristic genes related to inflammation during the progression of LTBI to ATB. The expression and diagnostic accuracy of these characteristic genes were subsequently verified. These genes were then used to develop diagnostic nomograms. In addition, single-cell expression clustering analysis, immune cell expression clustering analysis, GSVA analysis, immune cell correlation, and immune checkpoint correlation of characteristic genes were conducted. Furthermore, the upstream shared miRNA was predicted, and a miRNA-genes network was constructed. Candidate drugs were also analyzed and predicted. Results In comparison to LTBI, a total of 96 upregulated and 26 downregulated genes related to the inflammatory response were identified in ATB. These characteristic genes have demonstrated excellent diagnostic performance and significant correlation with many immune cells and immune sites. The results of the miRNA-genes network analysis suggested a potential role of hsa-miR-3163 in the molecular mechanism of LTBI progressing into ATB. Moreover, retinoic acid may offer a potential avenue for the prevention of LTBI progression to ATB and for the treatment of ATB. Conclusion Our research has identified key inflammatory response-related genes that are characteristic of LTBI progression to ATB and hsa-miR-3163 as a significant node in the molecular mechanism of this progression. Our analyses have demonstrated the excellent diagnostic performance of these characteristic genes and their significant correlation with many immune cells and immune checkpoints. The CD274 immune checkpoint presents a promising target for the prevention and treatment of ATB. Furthermore, our findings suggest that retinoic acid may have a role in preventing LTBI from progressing to ATB and in treating ATB. This study provides a new perspective for differential diagnosis of LTBI and ATB and may uncover potential inflammatory immune mechanisms, biomarkers, therapeutic targets, and effective drugs in the progression of LTBI into ATB.
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Affiliation(s)
- Shuai Ma
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443000, China
- College of Basic Medical Science, China Three Gorges University, Yichang 443000, China
| | - Peifei Peng
- Department of Geriatrics, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Zhihao Duan
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443000, China
- College of Basic Medical Science, China Three Gorges University, Yichang 443000, China
| | - Yifeng Fan
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443000, China
- College of Basic Medical Science, China Three Gorges University, Yichang 443000, China
| | - Xinzhi Li
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443000, China
- College of Basic Medical Science, China Three Gorges University, Yichang 443000, China
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Wang X, Liu W, Zhang D, Jiao Y, Zhao Q, Liu Y, Shi W, Bao Y. Salvia miltiorrhiza polysaccharides alleviate florfenicol-induced inflammation and oxidative stress in chick livers by regulating phagosome signaling pathway. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 249:114428. [PMID: 36516627 DOI: 10.1016/j.ecoenv.2022.114428] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 12/10/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
Florfenicol (FFC) is a commonly used antibiotic in animal breeding, especially in broiler breeding. Previous studies found that FFC could affect the liver function of chickens. However, the mechanisms underlying the effects of FFC on liver function are still not completely clear. Moreover, the research on drugs that antagonize FFC hepatotoxicity is relatively lacking. Salvia miltiorrhiza polysaccharides (SMPs) have been proved to have obvious liver protection effects. Therefore, we exposed chicks to FFC at the clinically recommended dose of 0.15 g/L. At the same time, 0.15 g/L FFC and 5 g/L SMPs were given to another group of chicks. After 5 days of continuous administration, the livers of chicks from different treatment groups were sequenced by transcriptome and proteome. Based on the analysis of sequencing data, we also focused on the detection of inflammation and oxidation indicators related to the phagosome signaling pathway with significant enrichment of differential factors in the livers of chicks. The results showed that some significantly differentially expressed genes and proteins induced by FFC were enriched in the phagosome signaling pathway, and they increased the expression levels of inflammatory factors and peroxides. However, SMPs intervention significantly reversed the tendency of FFC to alter phagosome signaling pathways and reduced the expression levels of inflammatory factors and peroxides. In conclusion, FFC caused liver inflammation and oxidative stress in chicks by regulating the phagosome signaling pathway. Meanwhile, SMPs could improve the adverse effects of FFC on the phagosome signaling pathway. This study provided new insights into the ameliorative effects and mechanisms of SMPs on hepatotoxicity of FFC.
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Affiliation(s)
- Xiao Wang
- College of Traditional Chinese Veterinary Medicine, Hebei Agricultural University, Baoding 071000, China
| | - Wei Liu
- College of Traditional Chinese Veterinary Medicine, Hebei Agricultural University, Baoding 071000, China
| | - Di Zhang
- College of Traditional Chinese Veterinary Medicine, Hebei Agricultural University, Baoding 071000, China
| | - Yulan Jiao
- College of Traditional Chinese Veterinary Medicine, Hebei Agricultural University, Baoding 071000, China; Hebei Provincial Veterinary Biotechnology Innovation Center, Baoding 071000, China; Ringpu (Baoding) Biological Pharmaceutical Co., Ltd, Baoding 071031, China
| | - Qianhui Zhao
- College of Traditional Chinese Veterinary Medicine, Hebei Agricultural University, Baoding 071000, China
| | - Ying Liu
- College of Traditional Chinese Veterinary Medicine, Hebei Agricultural University, Baoding 071000, China
| | - Wanyu Shi
- College of Traditional Chinese Veterinary Medicine, Hebei Agricultural University, Baoding 071000, China; Hebei Provincial Veterinary Biotechnology Innovation Center, Baoding 071000, China; Hebei Provincial Traditional Chinese Veterinary Medicine Technology Innovation Center, Baoding 071000, China.
| | - Yongzhan Bao
- College of Traditional Chinese Veterinary Medicine, Hebei Agricultural University, Baoding 071000, China; Hebei Provincial Veterinary Biotechnology Innovation Center, Baoding 071000, China.
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Huang Y, Ouyang F, Yang F, Zhang N, Zhao W, Xu H, Yang X. The expression of Hexokinase 2 and its hub genes are correlated with the prognosis in glioma. BMC Cancer 2022; 22:900. [PMID: 35982398 PMCID: PMC9386956 DOI: 10.1186/s12885-022-10001-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/10/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Hexokinase 2 (HK2) is an enzyme that catalyses the conversion of glucose to glucose-6-phosphate, which has been found to be associated with malignant tumour growth. However, the potential immunological and clinical significance of HK2, especially in terms of prognostic prediction for patients with glioma, has not been fully elucidated. METHODS To investigate the expression, immunological and clinical significance of HK2 in patients with glioma, several databases, including ONCOMINE, TIMER2.0, GEPIA, CGGA, UCSC, LinkedOmics, Metascape, STRING, GSCA, and TISIDB, as well as biochemical, cellular, and pathological analyses, were used in this study. In addition, we performed univariate, multivariate Cox regression and nomogram analyses of the hub genes positively and negatively correlated with HK2 to explore the potential regulatory mechanism in the initiation and development of glioma. RESULTS Our results demonstrated that HK2 was highly expressed in most malignant cancers. HK2 expression was significantly higher in lower grade glioma (LGG) and glioblastoma (GBM) than in adjacent normal tissue. In addition, HK2 expression was significantly correlated with clinical parameters, histological manifestations, and prognosis in glioma patients. Specifically, the data from The Cancer Genome Atlas downloaded from UCSC Xena database analysis showed that high expression of HK2 was strongly associated with poor prognosis in glioma patients. The LinkedOmics database indicated that HK2-related genes were mainly enriched in immune-related cells. In LGG and GBM tissues, HK2 expression is usually correlated with recognized immune checkpoints and the abundance of multiple immune infiltrates. Similarly, the Metascape database revealed that HK2-related genes were mainly enriched and annotated in immune-related pathways and immune cells. Further investigations also confirmed that the inhibition of HK2 expression remarkably suppressed metastasis and vasculogenic mimicry (VM) formation in glioma cells through regulating the gene expression of inflammatory and immune modulators. CONCLUSION HK2 expression was closely associated with the malignant properties of glioma through activating multiple immune-related signalling pathways to regulate immune responses and the infiltration of immune cells. Thus, HK2 and its hub genes may be a potential target for the treatment of glioma.
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Affiliation(s)
- Yishan Huang
- Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| | - Fan Ouyang
- Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| | - Fengxia Yang
- Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| | - Ning Zhang
- Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| | - Weijiang Zhao
- Cell Biology Department, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Hongwu Xu
- Department of Neurosurgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- Department of Anthropotomy/Clinically Oriented Anatomy, Shantou University Medical College, Shantou, China
| | - Xiaojun Yang
- Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou, China
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Monteiro MB, Patente TA, Mohammedi K, Queiroz MS, Azevedo MJ, Canani LH, Parisi MC, Marre M, Velho G, Corrêa-Giannella ML. Sex-specific associations of variants in regulatory regions of NADPH oxidase-2 (CYBB) and glutathione peroxidase 4 (GPX4) genes with kidney disease in type 1 diabetes. Free Radic Res 2013; 47:804-10. [PMID: 23919599 DOI: 10.3109/10715762.2013.828347] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Oxidative stress is involved in the pathophysiology of diabetic nephropathy. The superoxide-generating nicotinamide adenine dinucleotide phosphate-oxidase 2 (NOX2, encoded by the CYBB gene) and the antioxidant enzyme glutathione peroxidase 4 (GPX4) play opposing roles in the balance of cellular redox status. In the present study, we investigated associations of single nucleotide polymorphisms (SNPs) in the regulatory regions of CYBB and GPX4 with kidney disease in patients with type 1 diabetes. Two functional SNPs, rs6610650 (CYBB promoter region, chromosome X) and rs713041 (GPX4 3'untranslated region, chromosome 19), were genotyped in 451 patients with type 1 diabetes from a Brazilian cohort (diabetic nephropathy: 44.6%) and in 945 French/Belgian patients with type 1 diabetes from Genesis and GENEDIAB cohorts (diabetic nephropathy: 62.3%). The minor A-allele of CYBB rs6610650 was associated with lower estimated glomerular filtration rate (eGFR) in Brazilian women, and with the prevalence of established/advanced nephropathy in French/Belgian women (odds ratio 1.75, 95% CI 1.11-2.78, p = 0.016). The minor T-allele of GPX4 rs713041 was inversely associated with the prevalence of established/advanced nephropathy in Brazilian men (odds ratio 0.30, 95% CI 0.13-0.68, p = 0.004), and associated with higher eGFR in French/Belgian men. In conclusion, these heterogeneous results suggest that neither CYBB nor GPX4 are major genetic determinants of diabetic nephropathy, but nevertheless, they could modulate in a gender-specific manner the risk for renal disease in patients with type 1 diabetes.
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Affiliation(s)
- M B Monteiro
- Laboratório de Endocrinologia Celular e Molecular (LIM-25), Faculdade de Medicina da Universidade de São Paulo , São Paulo-SP , Brazil
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Tarazona-Santos E, Machado M, Magalhães WCS, Chen R, Lyon F, Burdett L, Crenshaw A, Fabbri C, Pereira L, Pinto L, Redondo RAF, Sestanovich B, Yeager M, Chanock SJ. Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: functional implications. Mol Biol Evol 2013; 30:2157-67. [PMID: 23821607 DOI: 10.1093/molbev/mst119] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The phagocyte NADPH oxidase catalyzes the reduction of O2 to reactive oxygen species with microbicidal activity. It is composed of two membrane-spanning subunits, gp91-phox and p22-phox (encoded by CYBB and CYBA, respectively), and three cytoplasmic subunits, p40-phox, p47-phox, and p67-phox (encoded by NCF4, NCF1, and NCF2, respectively). Mutations in any of these genes can result in chronic granulomatous disease, a primary immunodeficiency characterized by recurrent infections. Using evolutionary mapping, we determined that episodes of adaptive natural selection have shaped the extracellular portion of gp91-phox during the evolution of mammals, which suggests that this region may have a function in host-pathogen interactions. On the basis of a resequencing analysis of approximately 35 kb of CYBB, CYBA, NCF2, and NCF4 in 102 ethnically diverse individuals (24 of African ancestry, 31 of European ancestry, 24 of Asian/Oceanians, and 23 US Hispanics), we show that the pattern of CYBA diversity is compatible with balancing natural selection, perhaps mediated by catalase-positive pathogens. NCF2 in Asian populations shows a pattern of diversity characterized by a differentiated haplotype structure. Our study provides insight into the role of pathogen-driven natural selection in an innate immune pathway and sheds light on the role of CYBA in endothelial, nonphagocytic NADPH oxidases, which are relevant in the pathogenesis of cardiovascular and other complex diseases.
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Affiliation(s)
- Eduardo Tarazona-Santos
- Laboratory of Translational Genomics of the Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Gaithersburg, MD, USA.
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Machado M, Magalhães WC, Sene A, Araújo B, Faria-Campos AC, Chanock SJ, Scott L, Oliveira G, Tarazona-Santos E, Rodrigues MR. Phred-Phrap package to analyses tools: a pipeline to facilitate population genetics re-sequencing studies. INVESTIGATIVE GENETICS 2011; 2:3. [PMID: 21284835 PMCID: PMC3041995 DOI: 10.1186/2041-2223-2-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Accepted: 02/01/2011] [Indexed: 11/10/2022]
Abstract
Background Targeted re-sequencing is one of the most powerful and widely used strategies for population genetics studies because it allows an unbiased screening for variation that is suitable for a wide variety of organisms. Examples of studies that require re-sequencing data are evolutionary inferences, epidemiological studies designed to capture rare polymorphisms responsible for complex traits and screenings for mutations in families and small populations with high incidences of specific genetic diseases. Despite the advent of next-generation sequencing technologies, Sanger sequencing is still the most popular approach in population genetics studies because of the widespread availability of automatic sequencers based on capillary electrophoresis and because it is still less prone to sequencing errors, which is critical in population genetics studies. Two popular software applications for re-sequencing studies are Phred-Phrap-Consed-Polyphred, which performs base calling, alignment, graphical edition and genotype calling and DNAsp, which performs a set of population genetics analyses. These independent tools are the start and end points of basic analyses. In between the use of these tools, there is a set of basic but error-prone tasks to be performed with re-sequencing data. Results In order to assist with these intermediate tasks, we developed a pipeline that facilitates data handling typical of re-sequencing studies. Our pipeline: (1) consolidates different outputs produced by distinct Phred-Phrap-Consed contigs sharing a reference sequence; (2) checks for genotyping inconsistencies; (3) reformats genotyping data produced by Polyphred into a matrix of genotypes with individuals as rows and segregating sites as columns; (4) prepares input files for haplotype inferences using the popular software PHASE; and (5) handles PHASE output files that contain only polymorphic sites to reconstruct the inferred haplotypes including polymorphic and monomorphic sites as required by population genetics software for re-sequencing data such as DNAsp. Conclusion We tested the pipeline in re-sequencing studies of haploid and diploid data in humans, plants, animals and microorganisms and observed that it allowed a substantial decrease in the time required for sequencing analyses, as well as being a more controlled process that eliminates several classes of error that may occur when handling datasets. The pipeline is also useful for investigators using other tools for sequencing and population genetics analyses.
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Affiliation(s)
- Moara Machado
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av Antonio Carlos 6627, Pampulha, Caixa Postal 486, Belo Horizonte, MG, CEP 31270-910, Brazil
| | - Wagner Cs Magalhães
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av Antonio Carlos 6627, Pampulha, Caixa Postal 486, Belo Horizonte, MG, CEP 31270-910, Brazil
| | - Allan Sene
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av Antonio Carlos 6627, Pampulha, Caixa Postal 486, Belo Horizonte, MG, CEP 31270-910, Brazil
| | - Bruno Araújo
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av Antonio Carlos 6627, Pampulha, Caixa Postal 486, Belo Horizonte, MG, CEP 31270-910, Brazil
| | - Alessandra C Faria-Campos
- Departamento de Ciência da Computação, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Av Antonio Carlos 6627, Pampulha, Belo Horizonte, MG, CEP 31270-910, Brazil
| | - Stephen J Chanock
- Laboratory of Translational Genomics of the Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Gaithersburg, MD, USA.,8717 Grovemont Circle Advanced Technology Center, Room 127, Gaithersburg, MD, 20877, USA
| | - Leandro Scott
- Genomics and Computational Biology Group and Center for Excellence in Bioinformatics, René Rachou Institute, Fundação Oswaldo Cruz, Av Augusto de Lima 1715, Belo Horizonte, MG, 30190-002, Brazil
| | - Guilherme Oliveira
- Genomics and Computational Biology Group and Center for Excellence in Bioinformatics, René Rachou Institute, Fundação Oswaldo Cruz, Av Augusto de Lima 1715, Belo Horizonte, MG, 30190-002, Brazil
| | - Eduardo Tarazona-Santos
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av Antonio Carlos 6627, Pampulha, Caixa Postal 486, Belo Horizonte, MG, CEP 31270-910, Brazil
| | - Maira R Rodrigues
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av Antonio Carlos 6627, Pampulha, Caixa Postal 486, Belo Horizonte, MG, CEP 31270-910, Brazil
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Tarazona-Santos E, Fabbri C, Yeager M, Magalhaes WC, Burdett L, Crenshaw A, Pettener D, Chanock SJ. Diversity in the glucose transporter-4 gene (SLC2A4) in humans reflects the action of natural selection along the old-world primates evolution. PLoS One 2010; 5:e9827. [PMID: 20352120 PMCID: PMC2843742 DOI: 10.1371/journal.pone.0009827] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2009] [Accepted: 03/01/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Glucose is an important source of energy for living organisms. In vertebrates it is ingested with the diet and transported into the cells by conserved mechanisms and molecules, such as the trans-membrane Glucose Transporters (GLUTs). Members of this family have tissue specific expression, biochemical properties and physiologic functions that together regulate glucose levels and distribution. GLUT4 -coded by SLC2A4 (17p13) is an insulin-sensitive transporter with a critical role in glucose homeostasis and diabetes pathogenesis, preferentially expressed in the adipose tissue, heart muscle and skeletal muscle. We tested the hypothesis that natural selection acted on SLC2A4. METHODOLOGY/PRINCIPAL FINDINGS We re-sequenced SLC2A4 and genotyped 104 SNPs along a approximately 1 Mb region flanking this gene in 102 ethnically diverse individuals. Across the studied populations (African, European, Asian and Latin-American), all the eight common SNPs are concentrated in the N-terminal region upstream of exon 7 ( approximately 3700 bp), while the C-terminal region downstream of intron 6 ( approximately 2600 bp) harbors only 6 singletons, a pattern that is not compatible with neutrality for this part of the gene. Tests of neutrality based on comparative genomics suggest that: (1) episodes of natural selection (likely a selective sweep) predating the coalescent of human lineages, within the last 25 million years, account for the observed reduced diversity downstream of intron 6 and, (2) the target of natural selection may not be in the SLC2A4 coding sequence. CONCLUSIONS We propose that the contrast in the pattern of genetic variation between the N-terminal and C-terminal regions are signatures of the action of natural selection and thus follow-up studies should investigate the functional importance of different regions of the SLC2A4 gene.
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Affiliation(s)
- Eduardo Tarazona-Santos
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America.
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Amato R, Pinelli M, Monticelli A, Marino D, Miele G, Cocozza S. Genome-wide scan for signatures of human population differentiation and their relationship with natural selection, functional pathways and diseases. PLoS One 2009; 4:e7927. [PMID: 19936260 PMCID: PMC2775949 DOI: 10.1371/journal.pone.0007927] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Accepted: 10/26/2009] [Indexed: 11/22/2022] Open
Abstract
Genetic differences both between individuals and populations are studied for their evolutionary relevance and for their potential medical applications. Most of the genetic differentiation among populations are caused by random drift that should affect all loci across the genome in a similar manner. When a locus shows extraordinary high or low levels of population differentiation, this may be interpreted as evidence for natural selection. The most used measure of population differentiation was devised by Wright and is known as fixation index, or FST. We performed a genome-wide estimation of FST on about 4 millions of SNPs from HapMap project data. We demonstrated a heterogeneous distribution of FST values between autosomes and heterochromosomes. When we compared the FST values obtained in this study with another evolutionary measure obtained by comparative interspecific approach, we found that genes under positive selection appeared to show low levels of population differentiation. We applied a gene set approach, widely used for microarray data analysis, to detect functional pathways under selection. We found that one pathway related to antigen processing and presentation showed low levels of FST, while several pathways related to cell signalling, growth and morphogenesis showed high FST values. Finally, we detected a signature of selection within genes associated with human complex diseases. These results can help to identify which process occurred during human evolution and adaptation to different environments. They also support the hypothesis that common diseases could have a genetic background shaped by human evolution.
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Affiliation(s)
- Roberto Amato
- Gruppo Interdipartimentale di Bioinformatica e Biologia Computazionale, Università di Napoli Federico II-Università di Salerno, Naples, Italy.
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Luo Y, Gao W, Zhao X, Suo L, Chen L, Liu F, Song T, Chen J, Gao Y. Altered expression of mitochondrial related genes in the native Tibetan placents by mitochondrial cDNA array analysis. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/s1000-1948(09)60011-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Soares-Souza GB, Tarazona-Santos E, Chanock SJ. Characterization of a candidate locus for malaria susceptibility in human populations: a (TA)nmicrosatellite in the promoter region of the CYBB gene, the gp91phoxsubunit of the NADPH oxidase. Int J Immunogenet 2008; 35:107-9. [DOI: 10.1111/j.1744-313x.2008.00750.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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