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Simula ER, Jasemi S, Cossu D, Manca PC, Sanna D, Scarpa F, Meloni G, Cusano R, Sechi LA. The Genetic Landscape of Systemic Rheumatic Diseases: A Comprehensive Multigene-Panel Study Identifying Key Gene Polymorphisms. Pharmaceuticals (Basel) 2024; 17:438. [PMID: 38675400 PMCID: PMC11054024 DOI: 10.3390/ph17040438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Systemic rheumatic diseases, including conditions such as rheumatoid arthritis, Sjögren's syndrome, systemic sclerosis, and systemic lupus erythematosus, represent a complex array of autoimmune disorders characterized by chronic inflammation and diverse clinical manifestations. This study focuses on unraveling the genetic underpinnings of these diseases by examining polymorphisms in key genes related to their pathology. Utilizing a comprehensive genetic analysis, we have documented the involvement of these genetic variations in the pathogenesis of rheumatic diseases. Our study has identified several key polymorphisms with notable implications in rheumatic diseases. Polymorphism at chr11_112020916 within the IL-18 gene was prevalent across various conditions with a potential protective effect. Concurrently, the same IL18R1 gene polymorphism located at chr2_103010912, coding for the IL-18 receptor, was observed in most rheumatic conditions, reinforcing its potential protective role. Additionally, a further polymorphism in IL18R1 at chr2_103013408 seems to have a protective influence against the rheumatic diseases under investigation. In the context of emerging genes involved in rheumatic diseases, like PARK2, a significant polymorphism at chr6_161990516 was consistently identified across different conditions, exhibiting protective characteristics in these pathological contexts. The findings underscore the complexity of the genetic landscape in rheumatic autoimmune disorders and pave the way for a deeper understanding of their etiology and the possible development of more targeted and effective therapeutic strategies.
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Affiliation(s)
- Elena Rita Simula
- Dipartimento di Scienze Biomediche, Università di Sassari, 07100 Sassari, Italy; (E.R.S.); (S.J.); (D.C.); (D.S.); (F.S.)
| | - Seyedesomaye Jasemi
- Dipartimento di Scienze Biomediche, Università di Sassari, 07100 Sassari, Italy; (E.R.S.); (S.J.); (D.C.); (D.S.); (F.S.)
| | - Davide Cossu
- Dipartimento di Scienze Biomediche, Università di Sassari, 07100 Sassari, Italy; (E.R.S.); (S.J.); (D.C.); (D.S.); (F.S.)
| | - Pietro Carmelo Manca
- S.C. Servizio Immunotrasfusionale, Azienda Ospedaliero-Universitaria di Sassari, 07100 Sassari, Italy;
| | - Daria Sanna
- Dipartimento di Scienze Biomediche, Università di Sassari, 07100 Sassari, Italy; (E.R.S.); (S.J.); (D.C.); (D.S.); (F.S.)
| | - Fabio Scarpa
- Dipartimento di Scienze Biomediche, Università di Sassari, 07100 Sassari, Italy; (E.R.S.); (S.J.); (D.C.); (D.S.); (F.S.)
| | - Gianfranco Meloni
- Dipartimento di Medicina, Chirurgia e Farmacia, Università di Sassari, 07100 Sassari, Italy;
| | - Roberto Cusano
- Centro di Ricerca, Sviluppo, Studi Superiori in Sardegna (CRS4), Pula, 09100 Cagliari, Italy;
| | - Leonardo Antonio Sechi
- Dipartimento di Scienze Biomediche, Università di Sassari, 07100 Sassari, Italy; (E.R.S.); (S.J.); (D.C.); (D.S.); (F.S.)
- Struttura Complessa di Microbiologia e Virologia, Azienda Ospedaliera Universitaria, 07100 Sassari, Italy
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Cunha SMF, Lam S, Mallard B, Karrow NA, Cánovas Á. Genomic Regions Associated with Resistance to Gastrointestinal Nematode Parasites in Sheep-A Review. Genes (Basel) 2024; 15:187. [PMID: 38397178 PMCID: PMC10888242 DOI: 10.3390/genes15020187] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/27/2024] [Accepted: 01/27/2024] [Indexed: 02/25/2024] Open
Abstract
Gastrointestinal nematodes (GINs) can be a major constraint and global challenge to the sheep industry. These nematodes infect the small intestine and abomasum of grazing sheep, causing symptoms such as weight loss, diarrhea, hypoproteinemia, and anemia, which can lead to death. The use of anthelmintics to treat infected animals has led to GIN resistance, and excessive use of these drugs has resulted in residue traced in food and the environment. Resistance to GINs can be measured using multiple traits, including fecal egg count (FEC), Faffa Malan Chart scores, hematocrit, packed cell volume, eosinophilia, immunoglobulin (Ig), and dagginess scores. Genetic variation among animals exists, and understanding these differences can help identify genomic regions associated with resistance to GINs in sheep. Genes playing important roles in the immune system were identified in several studies in this review, such as the CFI and MUC15 genes. Results from several studies showed overlapping quantitative trait loci (QTLs) associated with multiple traits measuring resistance to GINs, mainly FEC. The discovery of genomic regions, positional candidate genes, and QTLs associated with resistance to GINs can help increase and accelerate genetic gains in sheep breeding programs and reveal the genetic basis and biological mechanisms underlying this trait.
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Affiliation(s)
- Samla Marques Freire Cunha
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Rd E, Guelph, ON N1G 2W1, Canada; (S.M.F.C.); (S.L.); (B.M.); (N.A.K.)
| | - Stephanie Lam
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Rd E, Guelph, ON N1G 2W1, Canada; (S.M.F.C.); (S.L.); (B.M.); (N.A.K.)
| | - Bonnie Mallard
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Rd E, Guelph, ON N1G 2W1, Canada; (S.M.F.C.); (S.L.); (B.M.); (N.A.K.)
- Department of Pathobiology, University of Guelph, 50 Stone Rd E, Guelph, ON N1G 2W1, Canada
| | - Niel A. Karrow
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Rd E, Guelph, ON N1G 2W1, Canada; (S.M.F.C.); (S.L.); (B.M.); (N.A.K.)
| | - Ángela Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Rd E, Guelph, ON N1G 2W1, Canada; (S.M.F.C.); (S.L.); (B.M.); (N.A.K.)
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Liao SY, Fingerlin T, Maier L. Genetic predisposition to sarcoidosis. J Autoimmun 2023:103122. [PMID: 37865580 DOI: 10.1016/j.jaut.2023.103122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/04/2023] [Indexed: 10/23/2023]
Abstract
Sarcoidosis is a complex systemic disease with clinical heterogeneity based on varying phenotypes and natural history. The detailed etiology of sarcoidosis remains unknown, but genetic predisposition as well as environmental exposures play a significant role in disease pathogenesis. We performed a comprehensive review of germline genetic (DNA) and transcriptomic (RNA) studies of sarcoidosis, including both previous studies and more recent findings. In this review, we provide an assessment of the following: genetic variants in sarcoidosis susceptibility and phenotypes, ancestry- and sex-specific genetic variants in sarcoidosis, shared genetic architecture between sarcoidosis and other diseases, and gene-environment interactions in sarcoidosis. We also highlight the unmet needs in sarcoidosis genetic studies, including the pressing requirement to include diverse populations and have consistent definitions of phenotypes in the sarcoidosis research community to help advance the application of genetic predisposition to sarcoidosis disease risk and manifestations.
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Affiliation(s)
- Shu-Yi Liao
- National Jewish Health, Department of Medicine, Denver, CO, USA; University of Colorado Anschutz Medical Campus, Department of Medicine, Aurora, CO, USA; Colorado School of Public Health, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA
| | - Tasha Fingerlin
- National Jewish Health, Department of Medicine, Denver, CO, USA; University of Colorado Anschutz Medical Campus, Department of Medicine, Aurora, CO, USA; Colorado School of Public Health, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA; National Jewish Health, Department of Immunology and Genomic Medicine, Denver, CO, USA
| | - Lisa Maier
- National Jewish Health, Department of Medicine, Denver, CO, USA; University of Colorado Anschutz Medical Campus, Department of Medicine, Aurora, CO, USA; Colorado School of Public Health, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA.
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Keng CT, Yogarajah T, Lee RCH, Muhammad IBH, Chia BS, Vasandani SR, Lim DS, Guo K, Wong YH, Mok CK, Chu JJH, Chew WL. AAV-CRISPR-Cas13 eliminates human enterovirus and prevents death of infected mice. EBioMedicine 2023; 93:104682. [PMID: 37390772 PMCID: PMC10363442 DOI: 10.1016/j.ebiom.2023.104682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/13/2023] [Accepted: 06/13/2023] [Indexed: 07/02/2023] Open
Abstract
BACKGROUND RNA viruses account for many human diseases and pandemic events but are often not targetable by traditional therapeutics modalities. Here, we demonstrate that adeno-associated virus (AAV) -delivered CRISPR-Cas13 directly targets and eliminates the positive-strand EV-A71 RNA virus in cells and infected mice. METHODS We developed a Cas13gRNAtor bioinformatics pipeline to design CRISPR guide RNAs (gRNAs) that cleave conserved viral sequences across the virus phylogeny and developed an AAV-CRISPR-Cas13 therapeutics using in vitro viral plaque assay and in vivo EV-A71 lethally-infected mouse model. FINDINGS We show that treatment with a pool of AAV-CRISPR-Cas13-gRNAs designed using the bioinformatics pipeline effectively blocks viral replication and reduces viral titers in cells by >99.99%. We further demonstrate that AAV-CRISPR-Cas13-gRNAs prophylactically and therapeutically inhibited viral replication in infected mouse tissues and prevented death in a lethally challenged EV-A71-infected mouse model. INTERPRETATION Our results show that the bioinformatics pipeline designs efficient CRISPR-Cas13 gRNAs for direct viral RNA targeting to reduce viral loads. Additionally, this new antiviral AAV-CRISPR-Cas13 modality represents an effective direct-acting prophylactic and therapeutic agent against lethal RNA viral infections. FUNDING Agency for Science, Technology and Research (A∗STAR) Assured Research Budget, A∗STAR Central Research Fund UIBR SC18/21-1089UI, A∗STAR Industrial Alignment Fund Pre-Positioning (IAF-PP) grant H17/01/a0/012, MOE Tier 2 2017 (MOE2017-T2-1-078; MOE-T2EP30221-0005), and NUHSRO/2020/050/RO5+5/NUHS-COVID/4.
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Affiliation(s)
- Choong Tat Keng
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore 138672, Singapore
| | - Thinesshwary Yogarajah
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Infectious Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Regina Ching Hua Lee
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Irfan Bin Hajis Muhammad
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore 138672, Singapore
| | - Bing Shao Chia
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore 138672, Singapore
| | - Suraj Rajan Vasandani
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore 138672, Singapore
| | - Daryl Shern Lim
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore 138672, Singapore
| | - Ke Guo
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore 138672, Singapore
| | - Yi Hao Wong
- NUSMed Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, 117599, Singapore
| | - Chee Keng Mok
- NUSMed Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, 117599, Singapore
| | - Justin Jang Hann Chu
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), 61 Biopolis Drive, Proteos #06-05, 138673, Singapore; Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Infectious Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore; NUSMed Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, 117599, Singapore.
| | - Wei Leong Chew
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore 138672, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 117596, Singapore.
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Zhang X, Yu H, Wang N, Li C. Comprehensive analysis of long noncoding RNAs and lncRNA-mRNA networks in snakehead (Channa argus) response to Nocardia seriolae infection. FISH & SHELLFISH IMMUNOLOGY 2023; 133:108558. [PMID: 36690266 DOI: 10.1016/j.fsi.2023.108558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 06/17/2023]
Abstract
Evidence has been demonstrated that lncRNAs are involved in a variety of immune responses in vertebrate. It has been demonstrated that immune-related lncRNAs play vital functions in immune regulation against infections in teleost. Nocardia seriolae, as one of the Gram-positive bacteria, can cause chronic systemic granulomatous disease for snakehead (Channa argus). However, how lncRNAs function in the immune regulation process once snakehead was infected with N. seriolae infection has not been studied so far. Accordingly, transcription landscapes of lncRNAs and mRNAs in snakehead were investigated. A total of 1,991 lncRNA were obtained. Totally, we predicted 57,584 co-expression and 16,047 co-location lncRNA-mRNA pairs. To further analyze the potential function of these lncRNAs, GO enrichment analysis and KEGG signal pathways were performed on the target mRNAs of these differently expressed lncRNAs, suggesting that lncRNAs may play essential roles in modulating mRNA expression levels, and subsequently trigger downstream immune signaling pathways to regulate the immune response in snakehead. In addition, 9 DEmRNA and 3 lncRNAs were randomly selected for qRT-PCR analyzed, which confirmed the accuracy of transcriptome data. These results can provide novel knowledge about lncRNAs in immune responses process in snakehead, and can serve as important resources for further investigating the roles of lncRNAs during pathogen infections in teleost.
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Affiliation(s)
- Xiaoyan Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Haohui Yu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ningning Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
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Effect of selected single nucleotide polymorphisms in SLC11A1, ANKRA2, IFNG and PGLYRP1 genes on host susceptibility to Mycobacterium avium subspecies paratuberculosis infection in Indian cattle. Vet Res Commun 2021; 46:209-221. [PMID: 34718924 DOI: 10.1007/s11259-021-09849-5] [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] [Received: 05/06/2021] [Accepted: 10/10/2021] [Indexed: 10/19/2022]
Abstract
Paratuberculosis (PTB) is a chronic infectious enteritis of ruminants, caused by Mycobacterium avium subspecies paratuberculosis (MAP) that brings huge economic loss to the dairy farmers. The study was conducted to explore the association of selected SNPs in IFNG, SLC11A1, ANKRA2 and PGLYRP1 genes with resistance to PTB disease in Indian cattle population. A case-control resource population was established based on the results of diagnostic tests used for detection of MAP infection status viz. ELISA, Johnin PPD test, faecal microscopy and IS900 blood PCR. The PCR-RFLP method was used for genotyping of SNPs. SNPs rs109453173 in SLC11A1, rs110853455 in IFNG and rs41933863 in ANKRA2 genes were significantly (P<0.05) associated with resistance to MAP infection. For SNP rs109453173, GG genotype and G allele was found to be associated with resistance against MAP infection than CC and CG genotypes and C allele, respectively. For SNP rs110853455, AG genotype was found to be associated with susceptibility to MAP infection than AA and GG genotype. For SNP rs41933863, the AG genotype provided three and six times more resistance against MAP infection than GG and AA genotype. The results of this study are suggestive of SNPs rs109453173, rs110853455 and rs41933863 as potential markers for screening MAP resistant cattle and a breeding programme favouring GG genotype and G allele for rs109453173, AG genotype for rs41933863 and against AG genotype for rs110853455 might confer resistance against MAP infection in Indian cattle. However, investigation of these SNPs in an independent and larger population will warrant the strength of association for resistance against MAP infection in cattle.
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Sfera A, Osorio C, Maguire G, Rahman L, Afzaal J, Cummings M, Maldonado JC. COVID-19, ferrosenescence and neurodegeneration, a mini-review. Prog Neuropsychopharmacol Biol Psychiatry 2021; 109:110230. [PMID: 33373681 PMCID: PMC7832711 DOI: 10.1016/j.pnpbp.2020.110230] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 02/06/2023]
Abstract
Exacerbation of cognitive, motor and nonmotor symptoms have been described in critically ill COVID-19 patients, indicating that, like prior pandemics, neurodegenerative sequelae may mark the aftermath of this viral infection. Moreover, SARS-CoV-2, the causative agent of COVID-19 disease, was associated with hyperferritinemia and unfavorable prognosis in older individuals, suggesting virus-induced ferrosenescence. We have previously defined ferrosenescence as an iron-associated disruption of both the human genome and its repair mechanisms, leading to premature cellular senescence and neurodegeneration. As viruses replicate more efficiently in iron-rich senescent cells, they may have developed the ability to induce this phenotype in host tissues, predisposing to both immune dysfunction and neurodegenerative disorders. In this mini-review, we summarize what is known about the SARS-CoV-2-induced cellular senescence and iron dysmetabolism. We also take a closer look at immunotherapy with natural killer cells, angiotensin II receptor blockers ("sartans"), iron chelators and dipeptidyl peptidase 4 inhibitors ("gliptins") as adjunct treatments for both COVID-19 and its neurodegenerative complications.
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Affiliation(s)
- Adonis Sfera
- Patton State Hospital, California, United States of America.
| | | | - Gerald Maguire
- University of California, Riverside, United States of America
| | - Leah Rahman
- Patton State Hospital, California, United States of America
| | - Jafri Afzaal
- Patton State Hospital, California, United States of America
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Zhuang G, Zeng Y, Tang Q, He Q, Luo G. Identifying M1 Macrophage-Related Genes Through a Co-expression Network to Construct a Four-Gene Risk-Scoring Model for Predicting Thyroid Cancer Prognosis. Front Genet 2020; 11:591079. [PMID: 33193731 PMCID: PMC7658400 DOI: 10.3389/fgene.2020.591079] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/28/2020] [Indexed: 12/18/2022] Open
Abstract
Macrophages are key innate immune cells in the tumor microenvironment that regulate primary tumor growth, vascularization, metastatic spread and response to therapies. Macrophages can polarize into two different states (M1 and M2) with distinct phenotypes and functions. To investigate the known tumoricidal effects of M1 macrophages, we obtained RNA expression profiles and clinical data from The Cancer Genome Atlas Thyroid Cancer (TCGA-THCA). The proportions of immune cells in tumor samples were assessed using CIBERSORT, and weighted gene co-expression network analysis (WGCNA) was used to identify M1 macrophage-related modules. Univariate Cox analysis and LASSO-Cox regression analysis were performed, and four genes (SPP1, DHRS3, SLC11A1, and CFB) with significant differential expression were selected through GEPIA. These four genes can be considered hub genes. The four-gene risk-scoring model may be an independent prognostic factor for THCA patients. The validation cohort and the entire cohort confirmed the results. Univariate and multivariate Cox analysis was performed to identify independent prognostic factors for THCA. Finally, a prognostic nomogram was built based on the entire cohort, and the nomogram combining the risk score and clinical prognostic factors was superior to the nomogram with individual clinical prognostic factors in predicting overall survival. Time-dependent ROC curves and DCA confirmed that the combined nomogram is useful. Gene set enrichment analysis (GSEA) was used to elucidate the potential molecular functions of the high-risk group. Our study identified four genes associated with M1 macrophages and established a prognostic nomogram that predicts overall survival for patients with THCA, which may help determine clinical treatment options for different patients.
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Affiliation(s)
- Gaojian Zhuang
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
| | - Yu Zeng
- Department of Thyroid and Neck Tumor, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Qun Tang
- Department of Pathology, Hunan University of Chinese Medicine, Changsha, China
| | - Qian He
- Department of Neurosurgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Guoqing Luo
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
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Contreras M, Karlsen M, Villar M, Olsen RH, Leknes LM, Furevik A, Yttredal KL, Tartor H, Grove S, Alberdi P, Brudeseth B, de la Fuente J. Vaccination with Ectoparasite Proteins Involved in Midgut Function and Blood Digestion Reduces Salmon Louse Infestations. Vaccines (Basel) 2020; 8:vaccines8010032. [PMID: 31963779 PMCID: PMC7157638 DOI: 10.3390/vaccines8010032] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/16/2020] [Accepted: 01/17/2020] [Indexed: 11/16/2022] Open
Abstract
Infestation with the salmon louse Lepeophtheirus salmonis (Copepoda, Caligidae) affects Atlantic salmon (Salmo salar L.) production in European aquaculture. Furthermore, high levels of salmon lice in farms significantly increase challenge pressure against wild salmon populations. Currently, available control methods for salmon louse have limitations, and vaccination appears as an attractive, environmentally sound strategy. In this study, we addressed one of the main limitations for vaccine development, the identification of candidate protective antigens. Based on recent advances in tick vaccine research, herein, we targeted the salmon louse midgut function and blood digestion for the identification of candidate target proteins for the control of ectoparasite infestations. The results of this translational approach resulted in the identification and subsequent evaluation of the new candidate protective antigens, putative Toll-like receptor 6 (P30), and potassium chloride, and amino acid transporter (P33). Vaccination with these antigens provided protection in Atlantic salmon by reducing adult female (P33) or chalimus II (P30) sea lice infestations. These results support the development of vaccines for the control of sea lice infestations.
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Affiliation(s)
- Marinela Contreras
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo s/n, 13005 Ciudad Real, Spain; (M.C.); (M.V.); (P.A.)
| | - Marius Karlsen
- Pharmaq AS, P.O. Box 267, Skoyen, N-0213 Oslo, Norway; (M.K.); (R.H.O.); (L.M.L.); (A.F.); (K.L.Y.)
| | - Margarita Villar
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo s/n, 13005 Ciudad Real, Spain; (M.C.); (M.V.); (P.A.)
- Biochemistry Section, Faculty of Science and Chemical Technologies, and Regional Centre for Biomedical Research (CRIB), University of Castilla-La Mancha, 13071 Ciudad Real, Spain
| | - Rolf Hetlelid Olsen
- Pharmaq AS, P.O. Box 267, Skoyen, N-0213 Oslo, Norway; (M.K.); (R.H.O.); (L.M.L.); (A.F.); (K.L.Y.)
| | - Lisa Marie Leknes
- Pharmaq AS, P.O. Box 267, Skoyen, N-0213 Oslo, Norway; (M.K.); (R.H.O.); (L.M.L.); (A.F.); (K.L.Y.)
| | - Anette Furevik
- Pharmaq AS, P.O. Box 267, Skoyen, N-0213 Oslo, Norway; (M.K.); (R.H.O.); (L.M.L.); (A.F.); (K.L.Y.)
| | - Karine Lindmo Yttredal
- Pharmaq AS, P.O. Box 267, Skoyen, N-0213 Oslo, Norway; (M.K.); (R.H.O.); (L.M.L.); (A.F.); (K.L.Y.)
| | - Haitham Tartor
- Norwegian Veterinary Institute, 0106 Oslo, Norway; (H.T.); (S.G.)
| | - Soren Grove
- Norwegian Veterinary Institute, 0106 Oslo, Norway; (H.T.); (S.G.)
- Institute of Marine Research, 5005 Bergen, Norway
| | - Pilar Alberdi
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo s/n, 13005 Ciudad Real, Spain; (M.C.); (M.V.); (P.A.)
| | - Bjorn Brudeseth
- Pharmaq AS, P.O. Box 267, Skoyen, N-0213 Oslo, Norway; (M.K.); (R.H.O.); (L.M.L.); (A.F.); (K.L.Y.)
- Correspondence: (B.B.); (J.d.l.F.)
| | - José de la Fuente
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ronda de Toledo s/n, 13005 Ciudad Real, Spain; (M.C.); (M.V.); (P.A.)
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078, USA
- Correspondence: (B.B.); (J.d.l.F.)
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Liu L, Liu W, Zheng Y, Chen J, Zhou J, Dai H, Cai S, Liu J, Zheng M, Ren Y. Anti-TNF- αtreatment-related pathways and biomarkers revealed by transcriptome analysis in Chinese psoriasis patients. BMC SYSTEMS BIOLOGY 2019; 13:29. [PMID: 30953507 PMCID: PMC6449888 DOI: 10.1186/s12918-019-0698-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Anti-tumor necrosis factor alpha (TNF- α) therapy has made a significant impact on treating psoriasis. Despite these agents being designed to block TNF- α activity, their mechanism of action in the remission of psoriasis is still not fully understood at the molecular level. RESULTS To better understand the molecular mechanisms of Anti-TNF- α therapy, we analysed the global gene expression profile (using mRNA microarray) in peripheral blood mononuclear cells (PBMCs) that were collected from 6 psoriasis patients before and 12 weeks after the treatment of etanercept. First, we identified 176 differentially expressed genes (DEGs) before and after treatment by using paired t-test. Then, we constructed the gene co-expression modules by weighted correlation network analysis (WGCNA), and 22 co-expression modules were found to be significantly correlated with treatment response. Of these 176 DEGs, 79 DEGs (M_DEGs) were the members of these 22 co-expression modules. Of the 287 GO functional processes and pathways that were enriched for these 79 M_DEGs, we identified 30 pathways whose overall gene expression activities were significantly correlated with treatment response. Of the original 176 DEGs, 19 (GO_DEGs) were found to be the members of these 30 pathways, whose expression profiles showed clear discrimination before and after treatment. As expected, of the biological processes and functionalities implicated by these 30 treatment response-related pathways, the inflammation and immune response was the top pathway in response to etanercept treatment, and some known TNF- α related pathways, such as molting cycle process, hair cycle process, skin epidermis development, regulation of hair follicle development, were implicated. Furthermore, additional novel pathways were also suggested, such as heparan sulfate proteoglycan metabolic process, vascular endothelial growth factor production, whose transcriptional regulation may mediate the response to etanercept treatment. CONCLUSION Through global gene expression analysis in PBMC of psoriasis patient and subsequent co-expression module based pathway analyses, we have identified a group of functionally coherent and differentially expressed genes (DEGs) and related pathways, which has not only provided new biological insight about the molecular mechanism of anti-TNF- α treatment, but also identified several genes whose expression profiles can be used as potential biomarkers for anti-TNF- α treatment response in psoriasis.
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Affiliation(s)
- Lunfei Liu
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenting Liu
- School of Public Health and Management, Hubei University of Medicine, Shiyan, Hubei, China.,Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Yuxin Zheng
- Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jisu Chen
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiong Zhou
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Huatuo Dai
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Suiqing Cai
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianjun Liu
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Min Zheng
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunqing Ren
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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11
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Gao M, Wang K, Yang M, Meng F, Lu R, Zhuang H, Cheng G, Wang X. Transcriptome Analysis of Bronchoalveolar Lavage Fluid From Children With Mycoplasma pneumoniae Pneumonia Reveals Natural Killer and T Cell-Proliferation Responses. Front Immunol 2018; 9:1403. [PMID: 29967623 PMCID: PMC6015898 DOI: 10.3389/fimmu.2018.01403] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 06/06/2018] [Indexed: 12/31/2022] Open
Abstract
Background Mycoplasma pneumoniae pneumonia (MPP) is one of the most common community-acquired pneumonia; this study is to explore the immune-pathogenesis of children MPP. Methods Next-generation transcriptome sequencing was performed on the bronchoalveolar lavage fluid cells from six children with MPP and three children with foreign body aspiration as control. Some of the results had been validated by quantitative real-time PCR in an expanded group of children. Results Results revealed 810 differentially expressed genes in MPP group comparing to control group, of which 412 genes including RLTPR, CARD11 and RASAL3 were upregulated. These upregulated genes were mainly enriched in mononuclear cell proliferation and signaling biological processes. Kyoto encyclopedia of genes and genomes pathway analysis revealed that hematopoietic cell linage pathway, natural killer cell-mediated cytotoxicity pathway, and T cell receptor signaling pathway were significantly upregulated in MPP children. In addition, significant alternative splicing events were found in GNLY and SLC11A1 genes, which may cause the differential expressions of these genes. Conclusion Our results suggest that NK and CD8+ T cells are over activated and proliferated in MPP children; the upregulated IFNγ, PRF1, GZMB, FASL, and GNLY may play important roles in the pathogenesis of children MPP.
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Affiliation(s)
- Man Gao
- Department of Pediatrics, The First Hospital of Jilin University, Changchun, China
| | - Kuo Wang
- Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, China
| | - Mingyue Yang
- Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, China
| | - Fanzheng Meng
- Department of Pediatrics, The First Hospital of Jilin University, Changchun, China
| | - Ruihua Lu
- Department of Pediatrics, The First Hospital of Jilin University, Changchun, China
| | - Huadong Zhuang
- Department of Pediatrics, The First Hospital of Jilin University, Changchun, China
| | - Genhong Cheng
- Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, China.,Department of Microbiology Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, United States
| | - Xiaosong Wang
- Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, China
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12
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Katiyar A, Sharma S, Singh TP, Kaur P. Identification of Shared Molecular Signatures Indicate the Susceptibility of Endometriosis to Multiple Sclerosis. Front Genet 2018; 9:42. [PMID: 29503661 PMCID: PMC5820528 DOI: 10.3389/fgene.2018.00042] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/30/2018] [Indexed: 01/21/2023] Open
Abstract
Women with endometriosis (EMS) appear to be at a higher risk of developing other autoimmune diseases predominantly multiple sclerosis (MS). Though EMS and MS are evidently diverse in their phenotype, they are linked by a common autoimmune condition or immunodeficiency which could play a role in the expansion of endometriosis and possibly increase the risk of developing MS in women with EMS. However, the common molecular links connecting EMS with MS are still unclear. We conducted a meta-analysis of microarray experiments focused on EMS and MS with their respective controls. The GEO2R web application discovered a total of 711 and 1516 genes that are differentially expressed across the experimental conditions in EMS and MS, respectively with 129 shared DEGs between them. The functional enrichment analysis of DEGs predicts the shared gene expression signatures as well as the overlapping biological processes likely to infer the co-occurrence of EMS with MS. Network based meta-analysis unveiled six interaction networks/crosstalks through overlapping edges between commonly dysregulated pathways of EMS and MS. The PTPN1, ERBB3, and CDH1 were observed to be the highly ranked hub genes connected with disease-related genes of both EMS and MS. Androgen receptor (AR) and nuclear factor-kB p65 (RelA) were observed to be the most enriched transcription factor in the upstream of shared down-regulated and up-regulated genes, respectively. The two disease sample sets compared through crosstalk interactions between shared pathways revealed commonly up- and down-regulated expressions of 10 immunomodulatory proteins as probable linkers between EMS and MS. This study pinpoints the number of shared genes, pathways, protein kinases, and upstream regulators that may help in the development of biomarkers for diagnosis of MS and endometriosis at the same time through improved understanding of shared molecular signatures and crosstalk.
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Affiliation(s)
- Amit Katiyar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Sujata Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Tej P Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
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13
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Abraham A, Naicy T, Raghavan KC, Siju J, Aravindakshan T. Evaluation of the association of SLC11A1 gene polymorphism with incidence of paratuberculosis in goats. J Genet 2017; 96:641-646. [DOI: 10.1007/s12041-017-0820-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Kanduc D, Shoenfeld Y. From HBV to HPV: Designing vaccines for extensive and intensive vaccination campaigns worldwide. Autoimmun Rev 2016; 15:1054-1061. [DOI: 10.1016/j.autrev.2016.07.030] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 07/12/2016] [Indexed: 12/12/2022]
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15
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Sun M, Zhang L, Shi S. Associations between NRAMP1 Polymorphisms and Susceptibility to Ulcerative Colitis/Crohn's Disease: A Meta-Analysis. Immunol Invest 2016; 45:255-70. [PMID: 27019053 DOI: 10.3109/08820139.2016.1149191] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVE Multiple environmental and genetic factors contribute to the risks of ulcerative colitis (UC) and Crohn's disease (CD). Several allelic variants have been identified in natural resistance associated macrophage protein 1 (NRAMP1) gene; however, their association with UC/CD remains conflicting. The purpose of this study was to evaluate whether NRAMP1 polymorphisms are associated with the susceptibility to UC/CD. METHODS A meta-analysis on the association between the NRAMP1 polymorphisms and susceptibility to UC/CD was performed. Relevant studies were retrieved from the databases. After eligible data were extracted, Mantel-Haenszel statistics and random/fixed effects model were applied to calculate the pooled odds radio (OR) and 95% confidence interval (95% CI). RESULTS Seven articles containing 536 UC cases, 997 CD cases, and 1361 controls were collected. No significant association between allele 2 frequency of NRAMP1 and susceptibility to UC/CD was detected in overall population (all p > 0.05). However, increased UC/CD risk for allele 3 was observed in Caucasian population (OR = 1.27, 95% CI = 1.08~1.50, p = 0.04), whereas decreased UC/CD risk was detected in non-Caucasian population (OR = 0.72, 95% CI = 0.60~0.87, p < 0.001), under "allele 3 vs. other alleles" model. Moreover, a significant increase in CD risk for T carrier frequency of -237 C/T (OR = 0.44, 95% CI, 0.26~0.75, p = 0.003) was detected, but not 274 C/T and 1729+55del4 (TGTG) +/del. CONCLUSIONS The polymorphism of -237 C/T is related to the risk of CD; and the association of allele 3 with UC/CD risk differs in Caucasian and non-Caucasian population, which might be the potential biomarkers for clinical diagnosis of UC/CD.
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Affiliation(s)
- Manyi Sun
- a Department of Gastroenterology , Tianjin Union Medicine Center & Tianjin People's Hospital , Tianjin , China
| | - Li Zhang
- b Department of Pathology , Tianjin Union Medicine Center & Tianjin People's Hospital , Tianjin , China
| | - Songli Shi
- b Department of Pathology , Tianjin Union Medicine Center & Tianjin People's Hospital , Tianjin , China
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16
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Yndart A, Kaushik A, Agudelo M, Raymond A, Atluri VS, Saxena SK, Nair M. Investigation of Neuropathogenesis in HIV-1 Clade B and C Infection Associated with IL-33 and ST2 Regulation. ACS Chem Neurosci 2015; 6:1600-12. [PMID: 26110635 DOI: 10.1021/acschemneuro.5b00156] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In present research work, for the first time, we demonstrate that neuropathogenesis in HIV-1 clade B and C infection is associated with IL-33 and ST2 dysregulation, that is, implication toward neuropathogenesis. It is known that neuropathogenesis of HIV infected individuals is clade dependent. Proinflammatory cytokines and related receptors play a significant role in the complex regulatory mechanisms of neuropathogenesis in HIV-1 infection. Among them, IL-33 is an inflammatory cytokine expressed in the central nervous system (CNS) and activates microglia cells and may affect neuroimmune inflammatory processes involved in HIV neuropathogenesis. Beside this, IL-33 receptor (ST2) plays a role in neuroinflammatory processes through the modulation of the biological action of IL-33. quantitative real time PCR (qRT-PCR), ELISA, Western blot (WB), and flow cytometry experiments were performed to elucidate the role of IL-33/ST2 in HIV neuropathogenesis in CNS cells. Apoptosis and mechanisms of IL-33 in neuronal cells were studied using caspase-3 assay and RT-PCR. Results of the studies suggest that the infection in CNS cells with HIV-1 clade B resulted in higher levels of IL-33/ST2L expression compared to HIV-1 clade C infection. Furthermore, higher concentrations of IL-33 were associated with a decrease in myocyte enhancer factor 2C (MEF2C) expression, a transcription factor that regulates synaptic function, and an increase in apoptosis, NOD2, and SLC11A1 in clade B infection. This led to neuroinflammation which dysregulates synaptic function and apoptosis. These parameters are common in neuroAIDS provoked by HIV infection.
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Affiliation(s)
- Adriana Yndart
- Center
of Personalized Nanomedicine, Institute of Neuropharmacology, Department
of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida 33199, United States
| | - Ajeet Kaushik
- Center
of Personalized Nanomedicine, Institute of Neuropharmacology, Department
of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida 33199, United States
| | - Marisela Agudelo
- Center
of Personalized Nanomedicine, Institute of Neuropharmacology, Department
of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida 33199, United States
| | - Andrea Raymond
- Center
of Personalized Nanomedicine, Institute of Neuropharmacology, Department
of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida 33199, United States
| | - Venkata S. Atluri
- Center
of Personalized Nanomedicine, Institute of Neuropharmacology, Department
of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida 33199, United States
| | - Shailendra K Saxena
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad 500007 (TS), India
| | - Madhavan Nair
- Center
of Personalized Nanomedicine, Institute of Neuropharmacology, Department
of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida 33199, United States
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17
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Li L, Xu Y, Yu CX. Proteomic analysis of serum of women with elevated Ca-125 to differentiate malignant from benign ovarian tumors. Asian Pac J Cancer Prev 2013; 13:3265-70. [PMID: 22994745 DOI: 10.7314/apjcp.2012.13.7.3265] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Clinically, elevated cancer antigen 125 (CA-125) in blood predicts tumor burden in a woman's body, especially in the ovary, but cannot differentiate between malignant or benign. We here used intensive modern proteomic approaches to identify predictive proteins in the serum of women with elevated CA-125 to differentiate malignant from benign ovarian tumors. We identified differentially expressed proteins in serum samples of ovarian cancer (OC) patients, benign ovarian tumor (BT) patients, and healthy control women using mass spectrometry-based quantitative proteomics. Both the OC and BT patients had elevated CA-125. Quantitation was achieved using isobaric tags for relative and absolute quantitation. We obtained 124 quantified differential serum proteins in OC compared with BT. Two proteins, apolipoprotein A-4 (APOA4) and natural resistance-associated macrophage 1, were verified using Western blotting. Proteome profiling applied to OC cases identified several differential serum proteins in the serum of women with elevated CA-125. A novel protein, APOA4, has the potential to be a marker for malignant tumor differentiation in the serum of women with elevated CA-125.
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Affiliation(s)
- Li Li
- Department of Gynecology, Affiliated Tumor Hospital, Xinjiang Medical University, Urumqi, China.
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18
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Taka S, Gazouli M, Politis PK, Pappa KI, Anagnou NP. Transcription factor ATF-3 regulates allele variation phenotypes of the human SLC11A1 gene. Mol Biol Rep 2012. [PMID: 23187734 DOI: 10.1007/s11033-012-2289-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Genetic polymorphisms in the human solute carrier family 11 member 1 (SLC11A1) gene predispose to susceptibility to infectious/inflammatory diseases and cancer. Human susceptibility to these diseases exhibits allelic association with a polymorphic regulatory Z-DNA-forming microsatellite of a (GT/AC)n repeat. The carriage of different alleles may influence chromatin remodeling and accessibility by transcription factors. Of particular importance is the binding site for the Activating Protein 1 (AP-1) elements, (ATF-3 and c-Jun), adjacent to the 5' sequence of the Z-DNA-forming polymorphism. The aim of the study was to characterize the transcriptional mechanisms controlling different alleles of SLC11A1 expression by ATF-3 and c-Jun. Allele 2, [T(GT)5AC(GT)5AC(GT)10GGCAGA(G)6], and Allele 3, [T(GT)5AC(GT)5AC(GT)9GGCAGA(G)6], were subcloned into the PGL2Basic vector. Transient transfections of THP-1 cells with the constructs, in the presence or absence of pATF-3 were preformed. Luciferase expression was determined. To document the recruitment of ATF-3 and c-Jun, to the polymorphic promoter alleles in vivo, we performed ChIP assays with transient transfected THP-1 cells treated with or without lipopolyssacharides. Our data documented that ATF-3 suppresses the transcriptional activation of Allele-3, and this suppression is enhanced in the presence of lipopolyssacharides. Our findings suggest that ATF-3 and c-Jun may influence heritable variation in SLC11A1-dependent innate resistance to infection and inflammation both within and between populations.
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Affiliation(s)
- Styliani Taka
- Laboratory of Biology, University of Athens School of Medicine, 176 Michalakopoulou Street, 115 27, Athens, Greece
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Ganguly I, Sharma A, Mitra A, Kumar N, Ganguly A. Analysis of genetic variations of complete TM4 of buffalo (Bubalus bubalis) Slc11A1 gene. JOURNAL OF APPLIED ANIMAL RESEARCH 2011. [DOI: 10.1080/09712119.2011.607943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Indrajit Ganguly
- a Genome Analysis Laboratory, Animal Genetics Division, Indian Veterinary Research Institute , Indian Council of Agricultural Research , Izatnagar, Bareilly, India
- c National Bureau of Animal Genetic Resources , Karnal, Haryana, 132001, India
| | - Arjava Sharma
- a Genome Analysis Laboratory, Animal Genetics Division, Indian Veterinary Research Institute , Indian Council of Agricultural Research , Izatnagar, Bareilly, India
| | - Abhijit Mitra
- a Genome Analysis Laboratory, Animal Genetics Division, Indian Veterinary Research Institute , Indian Council of Agricultural Research , Izatnagar, Bareilly, India
| | - Nishant Kumar
- a Genome Analysis Laboratory, Animal Genetics Division, Indian Veterinary Research Institute , Indian Council of Agricultural Research , Izatnagar, Bareilly, India
- d FVSc, SKUASTJ , RS.Pura, Jammu, 181102, India
| | - Anita Ganguly
- b Division of Biochemistry and Food Science , Indian Veterinary Research Institute, Indian Council of Agricultural Research , Izatnagar, Bareilly, India
- e Department of Veterinary Physiology and Biochemistry , COVS, LLRUVAS , Hisar, Haryana, 125004, India
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Neves JV, Wilson JM, Kuhl H, Reinhardt R, Castro LFC, Rodrigues PNS. Natural history of SLC11 genes in vertebrates: tales from the fish world. BMC Evol Biol 2011; 11:106. [PMID: 21501491 PMCID: PMC3103463 DOI: 10.1186/1471-2148-11-106] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 04/18/2011] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The SLC11A1/Nramp1 and SLC11A2/Nramp2 genes belong to the SLC11/Nramp family of transmembrane divalent metal transporters, with SLC11A1 being associated with resistance to pathogens and SLC11A2 involved in intestinal iron uptake and transferrin-bound iron transport. Both members of the SLC11 gene family have been clearly identified in tetrapods; however SLC11A1 has never been documented in teleost fish and is believed to have been lost in this lineage during early vertebrate evolution. In the present work we characterized the SLC11 genes in teleosts and evaluated if the roles attributed to mammalian SLC11 genes are assured by other fish specific SLC11 gene members. RESULTS Two different SLC11 genes were isolated in the European sea bass (Dicentrarchus. labrax), and named slc11a2-α and slc11a2-β, since both were found to be evolutionary closer to tetrapods SLC11A2, through phylogenetic analysis and comparative genomics. Induction of slc11a2-α and slc11a2-β in sea bass, upon iron modulation or exposure to Photobacterium damselae spp. piscicida, was evaluated in in vivo or in vitro experimental models. Overall, slc11a2-α was found to respond only to iron deficiency in the intestine, whereas slc11a2-β was found to respond to iron overload and bacterial infection in several tissues and also in the leukocytes. CONCLUSIONS Our data suggests that despite the absence of slc11a1, its functions have been undertaken by one of the slc11a2 duplicated paralogs in teleost fish in a case of synfunctionalization, being involved in both iron metabolism and response to bacterial infection. This study provides, to our knowledge, the first example of this type of sub-functionalization in iron metabolism genes, illustrating how conserving the various functions of the SLC11 gene family is of crucial evolutionary importance.
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Affiliation(s)
- João V Neves
- Iron and Innate Immunity, Instituto de Biologia Molecular e Celular (IBMC), Rua do Campo Alegre 823, 4150-180 Porto, Portugal
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Vacca GM, Pazzola M, Pisano C, Carcangiu V, Diaz ML, Nieddu M, Robledo R, Mezzanotte R, Dettori ML. Chromosomal localisation and genetic variation of the SLC11A1 gene in goats (Capra hircus). Vet J 2010; 190:60-5. [PMID: 21071245 DOI: 10.1016/j.tvjl.2010.09.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Revised: 09/15/2010] [Accepted: 09/30/2010] [Indexed: 12/20/2022]
Abstract
The solute carrier family 11 member A1 (SLC11A1) gene is associated with resistance to infectious diseases. Chromosomal localisation, genomic regions corresponding to functional domains and the genetic variability of microsatellites in the 3' untranslated region (3'-UTR) of this gene were investigated in 427 goats (Capra hircus) of six breeds. Using dual colour fluorescence in situ hybridisation, SLC11A1 was localised to goat chromosome 2. Single strand conformation polymorphism was used to screen for polymorphisms in SLC11A1 exons 2, 10 and 15. There was no variation among goat breeds in the sarcoma homology 3 (SH3) binding motif, the protein kinase C phosphorylation site or the two N-linked glycosylation sites. Exon 15 exhibited variability due to the presence of two polymorphic microsatellites. Genotyping of the upstream guanine-thymine repeat (GTn) at 3'-UTR revealed eight alleles (GT11, GT12, GT14-GT19) in goats, whereas GT13 (present in cattle) was absent. Most goats carried the GT16 allele and no allele was found to be exclusive to only one breed. The coefficient of genetic differentiation value (G(ST)) was 0.084. This microsatellite appears to be an informative DNA marker for genetic linkage analysis in goats.
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Affiliation(s)
- G M Vacca
- Dipartimento di Biologia Animale, Università degli Studi Sassari, 07100 Sassari, Italy.
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Teixeira VH, Olaso R, Martin-Magniette ML, Lasbleiz S, Jacq L, Oliveira CR, Hilliquin P, Gut I, Cornelis F, Petit-Teixeira E. Transcriptome analysis describing new immunity and defense genes in peripheral blood mononuclear cells of rheumatoid arthritis patients. PLoS One 2009; 4:e6803. [PMID: 19710928 PMCID: PMC2729373 DOI: 10.1371/journal.pone.0006803] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Accepted: 08/03/2009] [Indexed: 12/13/2022] Open
Abstract
Background Large-scale gene expression profiling of peripheral blood mononuclear cells from Rheumatoid Arthritis (RA) patients could provide a molecular description that reflects the contribution of diverse cellular responses associated with this disease. The aim of our study was to identify peripheral blood gene expression profiles for RA patients, using Illumina technology, to gain insights into RA molecular mechanisms. Methodology/Principal Findings The Illumina Human-6v2 Expression BeadChips were used for a complete genome-wide transcript profiling of peripheral blood mononuclear cells (PBMCs) from 18 RA patients and 15 controls. Differential analysis per gene was performed with one-way analysis of variance (ANOVA) and P values were adjusted to control the False Discovery Rate (FDR<5%). Genes differentially expressed at significant level between patients and controls were analyzed using Gene Ontology (GO) in the PANTHER database to identify biological processes. A differentially expression of 339 Reference Sequence genes (238 down-regulated and 101 up-regulated) between the two groups was observed. We identified a remarkably elevated expression of a spectrum of genes involved in Immunity and Defense in PBMCs of RA patients compared to controls. This result is confirmed by GO analysis, suggesting that these genes could be activated systemically in RA. No significant down-regulated ontology groups were found. Microarray data were validated by real time PCR in a set of nine genes showing a high degree of correlation. Conclusions/Significance Our study highlighted several new genes that could contribute in the identification of innovative clinical biomarkers for diagnostic procedures and therapeutic interventions.
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Affiliation(s)
- Vitor Hugo Teixeira
- GenHotel-EA3886, Evry University, Paris 7 University Medical School, AutoCure European Consortium member, Evry, France.
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Trombone APF, Ferreira SB, Raimundo FM, de Moura KCR, Avila-Campos MJ, Silva JS, Campanelli AP, De Franco M, Garlet GP. Experimental periodontitis in mice selected for maximal or minimal inflammatory reactions: increased inflammatory immune responsiveness drives increased alveolar bone loss without enhancing the control of periodontal infection. J Periodontal Res 2008; 44:443-51. [PMID: 18973535 DOI: 10.1111/j.1600-0765.2008.01133.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND AND OBJECTIVE Inflammatory immune reactions that occur in response to periodontopathogens are thought to protect the host against infection, but may trigger periodontal destruction. However, the molecular and genetic mechanisms underlying host susceptibility to periodontal infection and to periodontitis development have still not been established in detail. MATERIAL AND METHODS In this study, we examined the mechanisms that modulate the outcome of Aggregatibacter (Actinobacillus) actinomycetemcomitans-induced periodontal disease in mice mouse strains selected for maximal (AIRmax) or minimal (AIRmin) inflammatory reactions. RESULTS Our results showed that AIRmax mice developed a more severe periodontitis than AIRmin mice in response to A. actinomycetemcomitans infection, and this periodontitis was characterized by increased alveolar bone loss and inflammatory cell migration to periodontal tissues. In addition, enzyme-linked immunosorbent assays demonstrated that the levels of the cytokines interleukin-1beta, tumor necrosis factor-alpha and interleukin-17 were higher in AIRmax mice, as were the levels of matrix metalloproteinase (MMP)-2, MMP-13 and receptor activator of nuclear factor-kappaB ligand (RANKL) mRNA levels. However, the more intense inflammatory immune reaction raised by the AIRmax strain, in spite of the higher levels of antimicrobial mediators myeloperoxidase and inducible nitric oxide synthase, did not enhance the protective immunity to A. actinomycetemcomitans infection, because both AIRmax and AIRmin strains presented similar bacterial loads in periodontal tissues. In addition, the AIRmax strain presented a trend towards higher levels of serum C-reactive protein during the course of disease. CONCLUSION Our results demonstrate that the intensity of the inflammatory immune reaction is associated with the severity of experimental periodontitis, but not with the control of A. actinomycetemcomitans periodontal infection, suggesting that the occurrence of hyperinflammatory genotypes may not be an evolutionary advantage in the complex host-pathogen interaction observed in periodontal diseases.
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Affiliation(s)
- A P F Trombone
- Department of Biochemistry and Immunology, School of Medicine of Ribeirão Preto, FMRP/USP, SP, Brazil
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Gazouli M, Atsaves V, Mantzaris G, Economou M, Nasioulas G, Evangelou K, Archimandritis AJ, Anagnou NP. Role of functional polymorphisms of NRAMP1 gene for the development of Crohn's disease. Inflamm Bowel Dis 2008; 14:1323-30. [PMID: 18454481 DOI: 10.1002/ibd.20488] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
BACKGROUND Crohn's disease (CD) is characterized by chronic activation of macrophages. Natural resistance-associated macrophage protein 1 (NRAMP1) gene exerts many pleiotropic effects on macrophage functions. Hence, NRAMP1 may be also involved in the resistance to intracellular pathogens, and this effector of the innate immunity might be involved in CD pathogenesis. Polymorphic alleles at the NRAMP1 locus have been previously associated with susceptibility both to the putative infectious agents and to autoimmune disorders. Based on these indications, in the present study we investigate its candidacy as a genetic determinant for CD in a Greek population in an association-based study, comparing frequencies of 274 CD patients to these of 200 healthy control subjects. METHODS The 5'(GT)n promoter polymorphism and 9 either single nucleotide (SNPs) or insertion/deletion type polymorphisms were genotyped across the NRAMP1 gene. Reverse-transcriptase polymerase chain reaction (RT-PCR) and immunohistochemistry were performed in order to investigate the NRAMP1 mRNA levels in RNA isolated from biopsies of CD patients as well as protein expression in tissues. RESULTS Three NRAMP1 polymorphisms [5'(GT)n, D543N, and INT4G/C] were significantly associated with CD. Consistent with previous autoimmune disease studies, allele 3 at the functional 5'(GT)n promoter region repeat polymorphism, was significantly associated with CD when compared to healthy controls (odds ratio 1.50; 95% confidence interval [CI]: 1.16-1.95; P = 0.002). Interestingly, we observed that CD patients homozygous for allele 3 expressed higher NRAMP1 mRNA levels compared to carriers of allele 2. Furthermore, the protein levels of allele 3 carriers in tissues were also elevated compared to those of allele 2 carriers. Based on these data we can speculate that overrepresentation of allele 3 in CD patients could lead to hyperactivation of bowel-wall macrophages that are chronically exposed to lipopolysaccharide and this could subsequently cause the autoimmune-like phenotype characteristic of CD. CONCLUSIONS Collectively, our data indicate that genetic polymorphisms of NRAMP1 might be associated with susceptibility to CD.
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Affiliation(s)
- Maria Gazouli
- Department of Biology, School of Medicine, University of Athens, Greece.
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O'Brien BA, Archer NS, Simpson AM, Torpy FR, Nassif NT. Association of SLC11A1 promoter polymorphisms with the incidence of autoimmune and inflammatory diseases: A meta-analysis. J Autoimmun 2008; 31:42-51. [DOI: 10.1016/j.jaut.2008.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Revised: 02/07/2008] [Accepted: 02/08/2008] [Indexed: 10/22/2022]
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Marcucci G, Radmacher MD, Maharry K, Mrózek K, Ruppert AS, Paschka P, Vukosavljevic T, Whitman SP, Baldus CD, Langer C, Liu CG, Carroll AJ, Powell BL, Garzon R, Croce CM, Kolitz JE, Caligiuri MA, Larson RA, Bloomfield CD. MicroRNA expression in cytogenetically normal acute myeloid leukemia. N Engl J Med 2008; 358:1919-28. [PMID: 18450603 DOI: 10.1056/nejmoa074256] [Citation(s) in RCA: 334] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND A role of microRNAs in cancer has recently been recognized. However, little is known about the role of microRNAs in acute myeloid leukemia (AML). METHODS Using microRNA expression profiling, we studied samples of leukemia cells from adults under the age of 60 years who had cytogenetically normal AML and high-risk molecular features--that is, an internal tandem duplication in the fms-related tyrosine kinase 3 gene (FLT3-ITD), a wild-type nucleophosmin (NPM1), or both. A microRNA signature that was associated with event-free survival was derived from a training group of 64 patients and tested in a validation group of 55 patients. For the latter, a microRNA compound covariate predictor (called a microRNA summary value) was computed on the basis of weighted levels of the microRNAs forming the outcome signature. RESULTS Of 305 microRNA probes, 12 (including 5 representing microRNA-181 family members) were associated with event-free survival in the training group (P<0.005). In the validation group, the microRNA summary value was inversely associated with event-free survival (P=0.03). In multivariable analysis, the microRNA summary value remained associated with event-free survival (P=0.04) after adjustment for the allelic ratio of FLT3-ITD to wild-type FLT3 and for the white-cell count. Using results of gene-expression microarray analysis, we found that expression levels of the microRNA-181 family were inversely correlated with expression levels of predicted target genes encoding proteins involved in pathways of innate immunity mediated by toll-like receptors and interleukin-1beta. CONCLUSIONS A microRNA signature in molecularly defined, high-risk, cytogenetically normal AML is associated with the clinical outcome and with target genes encoding proteins involved in specific innate-immunity pathways.
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Affiliation(s)
- Guido Marcucci
- Division of Hematology and Oncology, Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA.
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