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Jin L, Macoritto M, Wang J, Bi Y, Wang F, Suarez-Fueyo A, Paez-Cortez J, Hu C, Knight H, Mascanfroni I, Staron MM, Schwartz Sterman A, Houghton JM, Westmoreland S, Tian Y. Multi-Omics Characterization of Colon Mucosa and Submucosa/Wall from Crohn's Disease Patients. Int J Mol Sci 2024; 25:5108. [PMID: 38791146 PMCID: PMC11121447 DOI: 10.3390/ijms25105108] [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: 02/02/2024] [Revised: 03/17/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
Crohn's disease (CD) is a subtype of inflammatory bowel disease (IBD) characterized by transmural disease. The concept of transmural healing (TH) has been proposed as an indicator of deep clinical remission of CD and as a predictor of favorable treatment endpoints. Understanding the pathophysiology involved in transmural disease is critical to achieving these endpoints. However, most studies have focused on the intestinal mucosa, overlooking the contribution of the intestinal wall in Crohn's disease. Multi-omics approaches have provided new avenues for exploring the pathogenesis of Crohn's disease and identifying potential biomarkers. We aimed to use transcriptomic and proteomic technologies to compare immune and mesenchymal cell profiles and pathways in the mucosal and submucosa/wall compartments to better understand chronic refractory disease elements to achieve transmural healing. The results revealed similarities and differences in gene and protein expression profiles, metabolic mechanisms, and immune and non-immune pathways between these two compartments. Additionally, the identification of protein isoforms highlights the complex molecular mechanisms underlying this disease, such as decreased RTN4 isoforms (RTN4B2 and RTN4C) in the submucosa/wall, which may be related to the dysregulation of enteric neural processes. These findings have the potential to inform the development of novel therapeutic strategies to achieve TH.
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Affiliation(s)
- Liang Jin
- AbbVie Bioresearch Center, Worcester, MA 01605, USA; (L.J.)
| | | | - Jing Wang
- Immunology Research, AbbVie, Cambridge, MA 02139, USA (A.S.-F.)
| | - Yingtao Bi
- AbbVie Bioresearch Center, Worcester, MA 01605, USA; (L.J.)
| | - Fei Wang
- AbbVie Bioresearch Center, Worcester, MA 01605, USA; (L.J.)
| | | | | | - Chenqi Hu
- Alnylam Pharmaceuticals, Cambridge, MA 02139, USA
| | - Heather Knight
- AbbVie Bioresearch Center, Worcester, MA 01605, USA; (L.J.)
| | | | | | | | - Jean Marie Houghton
- Division of Gastroenterology, Department of Medicine, UMass Chan Medical School, Worcester, MA 01655, USA;
| | | | - Yu Tian
- AbbVie Bioresearch Center, Worcester, MA 01605, USA; (L.J.)
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2
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Shi L, Li Y, Liu Q, Zhang L, Wang L, Liu X, Gao H, Hou X, Zhao F, Yan H, Wang L. Identification of SNPs and Candidate Genes for Milk Production Ability in Yorkshire Pigs. Front Genet 2021; 12:724533. [PMID: 34675963 PMCID: PMC8523896 DOI: 10.3389/fgene.2021.724533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 09/22/2021] [Indexed: 12/01/2022] Open
Abstract
Sow milk production ability is an important limiting factor impacting suboptimal growth and the survival of piglets. Through pig genetic improvement, litter sizes have been increased. Larger litters need more suckling mammary glands, which results in increased milk from the lactating sow. Hence, there is much significance to exploring sow lactation performance. For milk production ability, it is not practical to directly measure the milk yield, we used litter weight gain (LWG) throughout sow lactation as an indicator. In this study, we estimated the heritability of LWG, namely, 0.18 ± 0.07. We then performed a GWAS, and detected seven significant SNPs, namely, Sus scrofa Chromosome (SSC) 2: ASGA0010040 (p = 7.73E-11); SSC2:MARC0029355 (p = 1.30E-08), SSC6: WU_10.2_6_65751151 (p = 1.32E-10), SSC7: MARC0058875 (p = 4.99E-09), SSC10: WU_10.2_10_49571394 (p = 6.79E-08), SSC11: M1GA0014659 (p = 1.19E-07), and SSC15: MARC0042106 (p = 1.16E-07). We performed the distribution of phenotypes corresponding to the genotypes of seven significant SNPs and showed that ASGA0010040, MARC0029355, MARC0058875, WU_10.2_10_49571394, M1GA0014659, and MARC0042106 had extreme phenotypic values that corresponded to the homozygous genotypes, while the intermediate values corresponded to the heterozygous genotypes. We screened for flanking regions ± 200 kb nearby the seven significant SNPs, and identified 38 genes in total. Among them, 28 of the candidates were involved in lactose metabolism, colostrum immunity, milk protein, and milk fat by functional enrichment analysis. Through the combined analysis between 28 candidate genes and transcriptome data of the sow mammary gland, we found nine commons (ANO3, MUC15, DISP3, FBXO6, CLCN6, HLA-DRA, SLA-DRB1, SLA-DQB1, and SLA-DQA1). Furthermore, by comparing the chromosome positions of the candidate genes with the quantitative trait locus (QTLs) as previously reported, a total of 17 genes were found to be within 0.86–94.02 Mb of the reported QTLs for sow milk production ability, in which, NAV2 was found to be located with 0.86 Mb of the QTL region ssc2: 40936355. In conclusion, we identified seven significant SNPs located on SSC2, 6, 7, 10, 11, and 15, and propose 28 candidate genes for the ability to produce milk in Yorkshire pigs, 10 of which were key candidates.
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Affiliation(s)
- Lijun Shi
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yang Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qian Liu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Longchao Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ligang Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xin Liu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongmei Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinhua Hou
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fuping Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hua Yan
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lixian Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Fu Q, Agarwal D, Deng K, Matheson R, Yang H, Wei L, Ran Q, Deng S, Markmann JF. An Unbiased Machine Learning Exploration Reveals Gene Sets Predictive of Allograft Tolerance After Kidney Transplantation. Front Immunol 2021; 12:695806. [PMID: 34305931 PMCID: PMC8297499 DOI: 10.3389/fimmu.2021.695806] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/18/2021] [Indexed: 12/14/2022] Open
Abstract
Efforts at finding potential biomarkers of tolerance after kidney transplantation have been hindered by limited sample size, as well as the complicated mechanisms underlying tolerance and the potential risk of rejection after immunosuppressant withdrawal. In this work, three different publicly available genome-wide expression data sets of peripheral blood lymphocyte (PBL) from 63 tolerant patients were used to compare 14 different machine learning models for their ability to predict spontaneous kidney graft tolerance. We found that the Best Subset Selection (BSS) regression approach was the most powerful with a sensitivity of 91.7% and a specificity of 93.8% in the test group, and a specificity of 86.1% and a sensitivity of 80% in the validation group. A feature set with five genes (HLA-DOA, TCL1A, EBF1, CD79B, and PNOC) was identified using the BSS model. EBF1 downregulation was also an independent factor predictive of graft rejection and graft loss. An AUC value of 84.4% was achieved using the two-gene signature (EBF1 and HLA-DOA) as an input to our classifier. Overall, our systematic machine learning exploration suggests novel biological targets that might affect tolerance to renal allografts, and provides clinical insights that can potentially guide patient selection for immunosuppressant withdrawal.
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Affiliation(s)
- Qiang Fu
- Organ Transplantation Center, Sichuan Provincial People's Hospital and School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.,Center for Transplantation Sciences, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Divyansh Agarwal
- Division of Transplantation, Department of Surgery, Hospital of the University of Pennsylvania, Philadelphia, PA, United States
| | - Kevin Deng
- Center for Transplantation Sciences, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Rudy Matheson
- Center for Transplantation Sciences, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Hongji Yang
- Organ Transplantation Center, Sichuan Provincial People's Hospital and School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Liang Wei
- Organ Transplantation Center, Sichuan Provincial People's Hospital and School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Qing Ran
- Organ Transplantation Center, Sichuan Provincial People's Hospital and School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Shaoping Deng
- Organ Transplantation Center, Sichuan Provincial People's Hospital and School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - James F Markmann
- Center for Transplantation Sciences, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
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4
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Li H, Hou X, Liang Y, Xu F, Zhang X, Cui P, Xing G, Wang X, Jiang W. Gene-Based Tests of a Genome-Wide Association Study Dataset Highlight Novel Multiple Sclerosis Risk Genes. Front Neurosci 2021; 15:614528. [PMID: 34045940 PMCID: PMC8144314 DOI: 10.3389/fnins.2021.614528] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 04/14/2021] [Indexed: 01/09/2023] Open
Abstract
Multiple sclerosis (MS) is an autoimmune disorder influenced by genetic and environmental factors. Many studies have provided insights into genetic factors’ contribution to MS via large-scale genome-wide association study (GWAS) datasets. However, genetic variants identified to date do not adequately explain genetic risks for MS. This study hypothesized that novel MS risk genes could be identified by analyzing the MS-GWAS dataset using gene-based tests. We analyzed a GWAS dataset consisting of 9,772 MS cases and 17,376 healthy controls of European descent. We performed gene-based tests of 464,357 autosomal single nucleotide polymorphisms (SNPs) using two methods (PLINK and VEGAS2) and identified 28 shared genes satisfied p-value < 4.56 × 10–6. In further gene expression analysis, ten of the 28 genes were significantly differentially expressed in the MS case-control gene expression omnibus (GEO) database. GALC and HLA-DOB showed the most prominent differences in gene expression (two- and three-fold, respectively) between MS patients and healthy controls. In conclusion, our results reveal more information about MS hereditary characteristics and provide a basis for further studies.
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Affiliation(s)
- He Li
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Xiaodan Hou
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Yan Liang
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Fang Xu
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Xiyue Zhang
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Pan Cui
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Gebeili Xing
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China.,Department of Neurology, Inner Mongolia People's Hospital, Hohhot, China
| | - Xuejiao Wang
- Department of Neurology, Datong Third People's Hospital, Datong, China
| | - Wei Jiang
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China
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5
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Udhaya Kumar S, Madhana Priya N, Thirumal Kumar D, Anu Preethi V, Kumar V, Nagarajan D, Magesh R, Younes S, Zayed H, George Priya Doss C. An integrative analysis to distinguish between emphysema (EML) and alpha-1 antitrypsin deficiency-related emphysema (ADL)-A systems biology approach. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 127:315-342. [PMID: 34340772 DOI: 10.1016/bs.apcsb.2021.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Lung Emphysema is an abnormal enlargement of the air sacs followed by the destruction of alveolar walls without any prominent fibrosis. This study primarily identifies the differentially expressed genes (DEGs), interactions between them, and their significant involvement in the activated signaling cascades. The dataset with ID GSE1122 (five normal lung tissue samples, five of usual emphysema, and five of alpha-1 antitrypsin deficiency-related emphysema) from the gene expression omnibus (GEO) was analyzed using the GEO2R tool. The physical association between the DEGs were mapped using the STRING tool and was visualized in the Cytoscape software. The enriched functional processes were identified with the ClueGO plugin's help from Cytoscape. Further integrative functional annotation was performed by implying the GeneGo Metacore™ to distinguish the enriched pathway maps, process networks, and GO processes. The results from this analysis revealed the critical signaling cascades that have been either activated or inhibited due to identified DEGs. We found the activated pathways such as immune response IL-1 signaling pathway, positive regulation of smooth muscle migration, BMP signaling pathway, positive regulation of leukocyte migration, NIK/NF-kappB signaling, and cytochrome-c oxidase activity. Finally, we mapped four crucial genes (CCL5, ALK, TAC1, CD74, and HLA-DOA) by comparing the functional annotations that could be significantly influential in emphysema molecular pathogenesis. Our study provides insights into the pathogenesis of emphysema and helps in developing potential drug targets against emphysema.
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Affiliation(s)
- S Udhaya Kumar
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - N Madhana Priya
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai, Tamil Nadu, India
| | - D Thirumal Kumar
- Meenakshi Academy of Higher Education and Research, Chennai, Tamil Nadu, India
| | - V Anu Preethi
- School of Computer Science and Engineering, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Vibhaa Kumar
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Dhanushya Nagarajan
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - R Magesh
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai, Tamil Nadu, India
| | - Salma Younes
- Department of Biomedical Sciences, College of Health and Sciences, QU Health, Qatar University, Doha, Qatar
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, QU Health, Qatar University, Doha, Qatar
| | - C George Priya Doss
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India.
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6
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Association between tumor mutation burden and immune infiltration in ovarian cancer. Int Immunopharmacol 2020; 89:107126. [PMID: 33189611 DOI: 10.1016/j.intimp.2020.107126] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/02/2020] [Accepted: 10/17/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND It remains unclear whether the tumor mutation burden (TMB) or a TMB-related signature could be prognostic indicators in ovarian cancer (OC), as potential correlations with immune infiltrates and immunotherapy responsiveness remains poorly understood. METHODS Data of 941 OC patients were collected from three datasets, including 587, 260, and 94 patients from The Cancer Genome Atlas (TCGA), GSE32062, and the International Cancer Genome Consortium (ICGC), respectively. TMB was calculated and correlations with clinical outcomes, immune infiltrates, and immunotherapy responsiveness were investigated in the TCGA OC cohort. Weighted gene co-expression network analysis was performed to identify TMB-related genes. A TMB-related signature was constructed and validated. RESULTS Higher TMB was associated with better survival in the TCGA and ICGC OC cohorts. The high-TMB group had higher CD8+ T-cell infiltration than the low-TMB group. No significant correlation was found between TMB and immunotherapy response. Furthermore, we selected 8 prognostic and TMB-related genes to construct a TMB-related signature that could distinguish between the high- and low-risk patients; its predictive power was validated in the GSE32062 and ICGC datasets. SubMap analysis suggested that patients in the low-risk group might have a better response to anti-PD1 therapy. CONCLUSIONS We examined the prognostic value of TMB and its potential association with immune cell infiltration and immunotherapy responsiveness in OC. A TMB-related prognostic signature consisting of 8 genes was developed and verified, which might be a promising prognostic signature for the prognosis of OC patients.
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Graves AM, Virdis F, Morrison E, Álvaro-Benito M, Khan AA, Freund C, Golovkina TV, Denzin LK. Human Hepatitis B Viral Infection Outcomes Are Linked to Naturally Occurring Variants of HLA-DOA That Have Altered Function. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2020; 205:923-935. [PMID: 32690655 PMCID: PMC7415708 DOI: 10.4049/jimmunol.2000476] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/11/2020] [Indexed: 12/21/2022]
Abstract
HLA molecules of the MHC class II (MHCII) bind and present pathogen-derived peptides for CD4 T cell activation. Peptide loading of MHCII in the endosomes of cells is controlled by the interplay of the nonclassical MHCII molecules, HLA-DM (DM) and HLA-DO (DO). DM catalyzes peptide loading, whereas DO, an MHCII substrate mimic, prevents DM from interacting with MHCII, resulting in an altered MHCII-peptide repertoire and increased MHCII-CLIP. Although the two genes encoding DO (DOA and DOB) are considered nonpolymorphic, there are rare natural variants. Our previous work identified DOB variants that altered DO function. In this study, we show that natural variation in the DOA gene also impacts DO function. Using the 1000 Genomes Project database, we show that ∼98% of individuals express the canonical DOA*0101 allele, and the remaining individuals mostly express DOA*0102, which we found was a gain-of-function allele. Analysis of 25 natural occurring DOα variants, which included the common alleles, identified three null variants and one variant with reduced and nine with increased ability to modulate DM activity. Unexpectedly, several of the variants produced reduced DO protein levels yet efficiently inhibited DM activity. Finally, analysis of associated single-nucleotide polymorphisms genetically linked the DOA*0102 common allele, a gain-of-function variant, with human hepatitis B viral persistence. In contrast, we found that the DOα F114L null allele was linked with viral clearance. Collectively, these studies show that natural variation occurring in the human DOA gene impacts DO function and can be linked to specific outcomes of viral infections.
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Affiliation(s)
- Austin M Graves
- Child Health Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901
- Rutgers Graduate School of Biomedical Sciences, Piscataway, NJ 08854
| | - Francesca Virdis
- Child Health Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901
| | - Eliot Morrison
- Laboratory of Protein Biochemistry, Department of Biology, Chemistry and Pharmacy, Free University of Berlin, 14195 Berlin, Germany
| | - Miguel Álvaro-Benito
- Laboratory of Protein Biochemistry, Department of Biology, Chemistry and Pharmacy, Free University of Berlin, 14195 Berlin, Germany
| | - Aly A Khan
- Department of Pathology, The University of Chicago, Chicago, IL 60637
| | - Christian Freund
- Laboratory of Protein Biochemistry, Department of Biology, Chemistry and Pharmacy, Free University of Berlin, 14195 Berlin, Germany
| | | | - Lisa K Denzin
- Child Health Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901;
- Department of Pediatrics, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901; and
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901
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Chen DP, Chang SW, Wang PN, Hus FP, Tseng CP. Association between single nucleotide polymorphisms within HLA region and disease relapse for patients with hematopoietic stem cell transplantation. Sci Rep 2019; 9:13731. [PMID: 31551439 PMCID: PMC6760494 DOI: 10.1038/s41598-019-50111-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 09/04/2019] [Indexed: 11/23/2022] Open
Abstract
Disease relapse occurs in patients with leukemia even hematopoietic stem cell transplantation (HSCT) was performed with human leukocyte antigen (HLA)-matched donors. As revealed previously by Petersdorf et al., there are nine single nucleotide polymorphisms (SNPs) located in the HLA region that potentially modulate the efficacy of HSCT. In this study, we investigated whether or not the genomic variants 500 base pairs flanking the nine transplantation-related SNPs were related to the risk of post-HSCT relapse for patients with leukemia (n = 141). The genomic DNAs collected from 85 patients with acute myeloid leukemia (AML), 56 patients with acute lymphocytic leukemia (ALL), and their respective HLA-matched donors were subject to SNPs analysis, conferred by the mode of mismatch between donor-recipient pair or by recipient or donor genotype analysis. Seven SNPs were revealed to associate with the risk of relapse post-HSCT. For patients with AML, the increased risk of post-HSCT relapse was associated with the donor SNP of rs111394117 in the intron of NOTCH4 gene, and the recipient SNPs of rs213210 in the ring finger protein 1 (RING1) gene promoter, and rs17220087 and rs17213693 in the intron of HLA-DOB gene. For patients with ALL, the increased risk of post-HSCT relapse was associated with the donor SNP of rs213210 in the RING1 gene promoter, and the recipient SNPs of rs79327197 in the HLA-DOA gene promoter, rs2009658 in the telomeric end of lymphotoxin-alpha (LTA) gene, rs17220087 and rs17213693 in the intron of HLA-DOB gene, and rs2070120 in the 3′-UTR of HLA-DOB gene. This study sheds new insight into selecting better candidate donors for performing HSCT in patients with AML and ALL.
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Affiliation(s)
- Ding-Ping Chen
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Su-Wei Chang
- Clinical Informatics and Medical Statistics Research Center, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Po-Nan Wang
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Fang-Ping Hus
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Ching-Ping Tseng
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan. .,Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan. .,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan. .,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.
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9
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Ghanem E, Al Bitar S, Dib R, Kabrita CS. Sleep restriction alters the temporal expression of major histocompatibility complex class II molecules in murine lymphoid tissues. Behav Brain Res 2019; 362:152-159. [DOI: 10.1016/j.bbr.2019.01.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 01/10/2019] [Accepted: 01/10/2019] [Indexed: 01/27/2023]
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10
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Boekhoudt GH, McGrath AG, Swisher JFA, Feldman GM. Immune Complexes Suppress IFN-γ–Induced Responses in Monocytes by Activating Discrete Members of the SRC Kinase Family. THE JOURNAL OF IMMUNOLOGY 2014; 194:983-9. [DOI: 10.4049/jimmunol.1401649] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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11
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Monson NL, Ortega SB, Ireland SJ, Meeuwissen AJ, Chen D, Plautz EJ, Shubel E, Kong X, Li MK, Freriks LH, Stowe AM. Repetitive hypoxic preconditioning induces an immunosuppressed B cell phenotype during endogenous protection from stroke. J Neuroinflammation 2014; 11:22. [PMID: 24485041 PMCID: PMC3926678 DOI: 10.1186/1742-2094-11-22] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 01/13/2014] [Indexed: 12/16/2022] Open
Abstract
Background Repetitive hypoxic preconditioning (RHP) creates an anti-inflammatory phenotype that protects from stroke-induced injury for months after a 2-week treatment. The mechanisms underlying long-term tolerance are unknown, though one exposure to hypoxia significantly increased peripheral B cell representation. For this study, we sought to determine if RHP specifically recruited B cells into the protected ischemic hemisphere, and whether RHP could phenotypically alter B cells prior to stroke onset. Methods Adult, male SW/ND4 mice received RHP (nine exposures over 2 weeks; 8 to 11 % O2; 2 to 4 hours) or identical exposures to 21 % O2 as control. Two weeks following RHP, a 60-minute transient middle cerebral artery occlusion was induced. Standard techniques quantified CXCL13 mRNA and protein expression. Two days after stroke, leukocytes were isolated from brain tissue (70:30 discontinuous Percoll gradient) and profiled on a BD-FACS Aria flow cytometer. In a separate cohort without stroke, sorted splenic CD19+ B cells were isolated 2 weeks after RHP and analyzed on an Illumina MouseWG-6 V2 Bead Chip. Final gene pathways were determined using Ingenuity Pathway Analysis. Student’s t-test or one-way analysis of variance determined significance (P < 0.05). Results CXCL13, a B cell-specific chemokine, was upregulated in post-stroke cortical vessels of both groups. In the ischemic hemisphere, RHP increased B cell representation by attenuating the diapedesis of monocyte, macrophage, neutrophil and T cells, to quantities indistinguishable from the uninjured, contralateral hemisphere. Pre-stroke splenic B cells isolated from RHP-treated mice had >1,900 genes differentially expressed by microarray analysis. Genes related to B-T cell interactions, including antigen presentation, B cell differentiation and antibody production, were profoundly downregulated. Maturation and activation were arrested in a cohort of B cells from pre-stroke RHP-treated mice while regulatory B cells, a subset implicated in neurovascular protection from stroke, were upregulated. Conclusions Collectively, our data characterize an endogenous neuroprotective phenotype that utilizes adaptive immune mechanisms pre-stroke to protect the brain from injury post-stroke. Future studies to validate the role of B cells in minimizing injury and promoting central nervous system recovery, and to determine whether B cells mediate an adaptive immunity to systemic hypoxia that protects from subsequent stroke, are needed.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Ann M Stowe
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center at Dallas, 6000 Harry Hines Blvd, Dallas, TX 75390-8813, USA.
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12
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Li C, Jin L, Bai Y, Chen Q, Fu L, Yang M, Xiao H, Zhao G, Wang S. Genome-wide expression analysis in Down syndrome: insight into immunodeficiency. PLoS One 2012; 7:e49130. [PMID: 23155455 PMCID: PMC3498323 DOI: 10.1371/journal.pone.0049130] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 10/04/2012] [Indexed: 02/07/2023] Open
Abstract
Down syndrome (DS) is caused by triplication of Human chromosome 21 (Hsa21) and associated with an array of deleterious phenotypes, including mental retardation, heart defects and immunodeficiency. Genome-wide expression patterns of uncultured peripheral blood cells are useful to understanding of DS-associated immune dysfunction. We used a Human Exon microarray to characterize gene expression in uncultured peripheral blood cells derived from DS individuals and age-matched controls from two age groups: neonate (N) and child (C). A total of 174 transcript clusters (gene-level) with eight located on Hsa21 in N group and 383 transcript clusters including 56 on Hsa21 in C group were significantly dysregulated in DS individuals. Microarray data were validated by quantitative polymerase chain reaction. Functional analysis revealed that the dysregulated genes in DS were significantly enriched in two and six KEGG pathways in N and C group, respectively. These pathways included leukocyte trans-endothelial migration, B cell receptor signaling pathway and primary immunodeficiency, etc., which causally implicated dysfunctional immunity in DS. Our results provided a comprehensive picture of gene expression patterns in DS at the two developmental stages and pointed towards candidate genes and molecular pathways potentially associated with the immune dysfunction in DS.
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Affiliation(s)
- Chong Li
- School of Life Science, Fudan University, Shanghai, China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Lei Jin
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Yun Bai
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Qimin Chen
- Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lijun Fu
- Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Minjun Yang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Huasheng Xiao
- National Engineering Center for Biochip at Shanghai, Shanghai, China
| | - Guoping Zhao
- School of Life Science, Fudan University, Shanghai, China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Shengyue Wang
- School of Life Science, Fudan University, Shanghai, China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
- * E-mail:
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13
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CIITA promoter I CARD-deficient mice express functional MHC class II genes in myeloid and lymphoid compartments. Genes Immun 2012; 13:299-310. [PMID: 22218223 PMCID: PMC3366023 DOI: 10.1038/gene.2011.86] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Three distinct promoters control the master regulator of MHC class II expression, CIITA, in a cell type specific manner. Promoter I (pI) CIITA, expressed primarily by dendritic cells and macrophages, expresses a unique isoform that contains a caspase recruitment domain. The activity and function of this isoform is not understood but has been thought to enhance the function of CIITA in antigen presenting cells. To determine if isoform I of CIITA has specific functions, CIITA mutant mice were created in which isoform I was replaced with isoform III sequences. Mice in which pI and the CARD encoding exon were deleted were also created. No defect in the formation of CD4 T cells, the ability to respond to a model antigen, or bacterial or viral challenge was observed in mice lacking CIITA isoform I. Although CIITA and MHC-II expression was decreased in splenic DC, the pI knockout animals expressed CIITA from downstream promoters, suggesting that control of pI activity is mediated by unknown s II distal elements that could act at the pIII, the B cell promoter. Thus, no critical function is linked to the CARD domain of CIITA isoform I with respect to basic immune system development, function and challenge.
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14
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Majumder P, Boss JM. CTCF controls expression and chromatin architecture of the human major histocompatibility complex class II locus. Mol Cell Biol 2010; 30:4211-23. [PMID: 20584980 PMCID: PMC2937552 DOI: 10.1128/mcb.00327-10] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2010] [Revised: 04/22/2010] [Accepted: 06/17/2010] [Indexed: 11/20/2022] Open
Abstract
The major histocompatibility complex class II (MHC-II) locus includes a dense cluster of genes that function to initiate immune responses. Expression of insulator CCCTC binding factor (CTCF) was found to be required for expression of all MHC class II genes associated with antigen presentation. Ten CTCF sites that divide the MHC-II locus into apparent evolutionary domains were identified. To define the role of CTCF in mediating regulation of the MHC II genes, chromatin conformation capture assays, which provide an architectural assessment of a locus, were conducted across the MHC-II region. Depending on whether MHC-II genes and the class II transactivator (CIITA) were being expressed, two CTCF-dependent chromatin architectural states, each with multiple configurations and interactions, were observed. These states included the ability to express MHC-II gene promoter regions to interact with nearby CTCF sites and CTCF sites to interact with each other. Thus, CTCF organizes the MHC-II locus into a novel basal architecture of interacting foci and loop structures that rearranges in the presence of CIITA. Disruption of the rearranged states eradicated expression, suggesting that the formation of these structures is key to coregulation of MHC-II genes and the locus.
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Affiliation(s)
- Parimal Majumder
- Department of Microbiology and Immunology, Emory University, 1510 Clifton Road, Atlanta, Georgia 30322
| | - Jeremy M. Boss
- Department of Microbiology and Immunology, Emory University, 1510 Clifton Road, Atlanta, Georgia 30322
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15
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Landsverk OJB, Bakke O, Gregers TF. MHC II and the endocytic pathway: regulation by invariant chain. Scand J Immunol 2009; 70:184-93. [PMID: 19703008 DOI: 10.1111/j.1365-3083.2009.02301.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The major histocompatibility complex (MHC) class I and II molecules perform vital functions in innate and adaptive immune responses towards invading pathogens. MHC class I molecules load peptides in the endoplasmatic reticulum (ER) and display them to the T cell receptors (TcR) on CD8(+) T lymphocytes. MHC class II molecules (MHC II) acquire their peptides in endosomes and present these to the TcR on CD4+ T lymphocytes. They are vital for the generation of humoral immune responses. MHC II assembly in the ER and trafficking to endosomes is guided by a specialized MHC II chaperone termed the invariant chain (Ii). Ii self-associates into a trimer in the ER, this provides a scaffold for the assembly of three MHC II heterodimers and blocks their peptide binding grooves, thereby avoiding premature peptide binding. Ii then transports the nascent MHC II to more or less specialized compartment where they can load peptides derived from internalized pathogens.
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Affiliation(s)
- O J B Landsverk
- Centre for Immune Regulation, Department of Molecular Biosciences, University of Oslo, 0316 Oslo, Norway
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16
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Seguín-Estévez Q, De Palma R, Krawczyk M, Leimgruber E, Villard J, Picard C, Tagliamacco A, Abbate G, Gorski J, Nocera A, Reith W. The transcription factor RFX protects MHC class II genes against epigenetic silencing by DNA methylation. THE JOURNAL OF IMMUNOLOGY 2009; 183:2545-53. [PMID: 19620312 DOI: 10.4049/jimmunol.0900376] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Classical and nonclassical MHC class II (MHCII) genes are coregulated by the transcription factor RFX (regulatory factor X) and the transcriptional coactivator CIITA. RFX coordinates the assembly of a multiprotein "enhanceosome" complex on MHCII promoters. This enhanceosome serves as a docking site for the binding of CIITA. Whereas the role of the enhanceosome in recruiting CIITA is well established, little is known about its CIITA-independent functions. A novel role of the enhanceosome was revealed by the analysis of HLA-DOA expression in human MHCII-negative B cell lines lacking RFX or CIITA. HLA-DOA was found to be reactivated by complementation of CIITA-deficient but not RFX-deficient B cells. Silencing of HLA-DOA was associated with DNA methylation at its promoter, and was relieved by the demethylating agent 5-azacytidine. Surprisingly, DNA methylation was also established at the HLA-DRA and HLA-DQB loci in RFX-deficient cells. This was a direct consequence of the absence of RFX, as it could be reversed by restoring RFX function. DNA methylation at the HLA-DOA, HLA-DRA, and HLA-DQB promoters was observed in RFX-deficient B cells and fibroblasts, but not in CIITA-deficient B cells and fibroblasts, or in wild-type fibroblasts, which lack CIITA expression. These results indicate that RFX and/or enhanceosome assembly plays a key CIITA-independent role in protecting MHCII promoters against DNA methylation. This function is likely to be crucial for retaining MHCII genes in an open chromatin configuration permissive for activation in MHCII-negative cells, such as the precursors of APC and nonprofessional APC before induction with IFN-gamma.
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17
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Souwer Y, Chamuleau MED, van de Loosdrecht AA, Tolosa E, Jorritsma T, Muris JJF, Dinnissen-van Poppel MJ, Snel SN, van de Corput L, Ossenkoppele GJ, Meijer CJLM, Neefjes JJ, Marieke van Ham S. Detection of aberrant transcription of major histocompatibility complex class II antigen presentation genes in chronic lymphocytic leukaemia identifies HLA-DOA mRNA as a prognostic factor for survival. Br J Haematol 2009; 145:334-43. [PMID: 19245431 DOI: 10.1111/j.1365-2141.2009.07625.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In human B cells, effective major histocompatibility complex (MHC) class II-antigen presentation depends not only on MHC class II, but also on the invariant chain (CD74 or Ii), HLA-DM (DM) and HLA-DO (DO), the chaperones regulating the antigen loading process of MHC class II molecules. We analysed immediate ex vivo expression of HLA-DR (DR), CD74, DM and DO in B cell chronic lymphocytic leukaemia (B-CLL). Real-time reverse transcription polymerase chain reaction demonstrated a highly significant upregulation of DRA, CD74, DMB, DOA and DOB mRNA in purified malignant cells compared to B cells from healthy donors. The increased mRNA levels were not translated into enhanced protein levels but could reflect aberrant transcriptional regulation. Indeed, upregulation of DRA, DMB, DOA and DOB mRNA correlated with enhanced expression of class II transactivator (CIITA). In-depth analysis of the various CIITA transcripts demonstrated a significant increased activity of the interferon-gamma-inducible promoter CIITA-PIV in B-CLL. Comparison of the aberrant mRNA levels with clinical outcome identified DOA mRNA as a prognostic indicator for survival. Multivariate analysis revealed that the prognostic value of DOA mRNA was independent of the mutational status of the IGHV genes. Thus, aberrant transcription of DOA forms a novel and additional prognostic indicator for survival in B-CLL.
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Affiliation(s)
- Yuri Souwer
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Academical Medical Centre, University of Amsterdam, Amsterdam, The Netherlands.
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18
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Pollack BP, Sapkota B, Boss JM. Ultraviolet radiation-induced transcription is associated with gene-specific histone acetylation. Photochem Photobiol 2008; 85:652-62. [PMID: 19076306 DOI: 10.1111/j.1751-1097.2008.00485.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
UVR is an important environmental carcinogen and a powerful modulator of the cutaneous immune system. Exposure to UVR activates many signaling pathways leading to changes in the expression of several hundred genes. While the covalent modification of histones has been shown to play a central role in regulating gene expression, the impact of UVR on histone modifications and the contribution of histone acetyltransferases (HATs) and histone deacetylases (HDACs) to the UVR-induced transcriptional response have not been completely characterized. In this report, we have examined the impact of UVR on histone H3 K9/14 acetylation. The potential role of UVR-induced histone acetylation in the UVR transcriptional response was also explored using the HAT inhibitor curcumin and HDAC inhibitor trichostatin A (TSA). We found that UVR caused an increase in histone H3 acetylation within the promoter regions of ATF3, COX2, IL-8, MKP1 and MnSOD. In most of the regions examined, histone H3 acetylation peaked 24 h after UVR and then returned to baseline levels by 72 h. The induction of ATF3, COX2 and MKP1 was blocked in the presence of curcumin at doses that decrease in vivo histone H3 acetylation but not at lower doses that do not affect acetylation levels. We also provide evidence that for ATF3, a transcriptional superinduction occurs after repeat exposures to UVR that can be recapitulated when the second UVR exposure is replaced with TSA treatment. Thus, UVR can alter histone acetylation within human keratinocytes and these changes may contribute to the UVR-transcriptional response.
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Affiliation(s)
- Brian P Pollack
- Department of Dermatology, Emory University School of Medicine, Atlanta, GA, USA.
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19
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MHC class II antigen presentation and immunological abnormalities due to deficiency of MHC class II and its associated genes. Exp Mol Pathol 2008; 85:40-4. [PMID: 18547561 DOI: 10.1016/j.yexmp.2008.03.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2008] [Accepted: 03/02/2008] [Indexed: 11/24/2022]
Abstract
Antigen presentation by Major Histocompatibility Complex (MHC) class II molecules plays an important role in controlling immunity and autoimmunity. Multiple co-factors including the invariant chain (Ii), HLA-DM and HLA-DO are involved in this process. While the role for Ii and DM has been well defined, the biological function of DO remains obscure. Our data indicate that DO inhibits presentation of endogenous self-antigens and that developmentally-regulated DO expression enables antigen presenting cells to preferentially present different sources of peptide antigens at different stages of development. Disruption of this regulatory mechanism can result in not only immunodeficiency but also autoimmunity. Despite the fact that deletion of each of the three genes in experimental animals is associated with profound immunological abnormalities, no corresponding human diseases have been reported. This discrepancy suggests the possibility that primary immunodeficiencies due to a genetic defect of Ii, DM and DO in humans are under diagnosed or diagnosed as "common variable immunodeficiency", a category of immunodeficiency of heterogeneous or undefined etiology. Clinical tests for any of these potential genetic defects are not yet available. We propose the use of multi-color flow cytometry in conjunction with intracellular staining to detect expression of Ii, DM, DO in peripheral blood B cells as a convenient reliable screening test to identify individuals with defects in antigen presentation.
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20
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Interleukin-27 upregulates major histocompatibility complex class II expression in primary human endothelial cells through induction of major histocompatibility complex class II transactivator. Hum Immunol 2007; 68:965-72. [PMID: 18191724 DOI: 10.1016/j.humimm.2007.10.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2007] [Revised: 09/26/2007] [Accepted: 10/05/2007] [Indexed: 11/24/2022]
Abstract
Interleukin-27 (IL-27) is a novel IL-12 family member that plays a critical role in the regulation of T-cell responses. Its immunoregulatory effects on endothelial cells (EC) remain unexplored. Here we show a role for IL-27 in the induction of major histocompatibility complex (MHC) expression in primary human EC. Stimulation of human umbilical vein ECs by IL-27 rapidly induces IFN regulatory factor-1 and dramatically increases the expression of major histocompatibility class II transactivator (CIITA) isoform IV. Expression of this transactivator correlates with increased MHC class II gene expression. IL-27 also enhances expression of MHC class I molecules. Furthermore expression of beta2-microglobulin and transporter associated with antigen processing-1 transcripts increases in response to IL-27. Additional microarray analysis demonstrates that IL-27 significantly upregulates a panel of genes that correlates with immune regulation, including the chemokines CXCL9, CXCL10, and CX3CL1 in human umbilical vein ECs. This first demonstration that both MHC II and I expression are increased in EC after IL-27 stimulation suggests that IL-27 may be important in conferring immune function on vascular endothelium.
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21
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van der Stoep N, Quinten E, Alblas G, Plancke A, van Eggermond MCJA, Holling TM, van den Elsen PJ. Constitutive and IFNgamma-induced activation of MHC2TA promoter type III in human melanoma cell lines is governed by separate regulatory elements within the PIII upstream regulatory region. Mol Immunol 2006; 44:2036-46. [PMID: 17067677 DOI: 10.1016/j.molimm.2006.09.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2006] [Revised: 09/11/2006] [Accepted: 09/12/2006] [Indexed: 11/28/2022]
Abstract
Cell lines established from tumor tissue of cutaneous melanoma biopsies often display constitutive and IFNgamma-inducible expression of MHC class II molecules. The expression of MHC class II molecules in melanoma is associated with an overall poor prognosis and unfavorable clinical outcome. We have analyzed the DNA elements and interacting transcription factors that control the constitutive and IFNgamma-inducible expression of the class II transactivator (CIITA), a co-activator essential for transcription of all MHC class II genes. Our studies reveal the activation of multiple CIITA promoter regions (CIITA-PII, -PIII and -PIV) in melanoma cell lines for both the constitutive and IFNgamma-inducible expression of MHC class II molecules. Furthermore, we show that constitutive and IFNgamma-inducible expression of the CIITA-PIII isoform is governed by separate regulatory elements within the PIII upstream regulatory region (PURR). Similarly constitutive activation in melanoma of CIITA-PII, CIITA-PIII, and CIITA-PIV does not require components of the IFNgamma signaling pathway. However, these components are readily recruited to the PURR and CIITA-PIV after exposure of cells to IFNgamma and account for the IFNgamma-induced expression of CIITA. Together, our data reveal the contribution of distinct elements and factors in the constitutive and IFNgamma-inducible expression of CIITA in melanoma cell lines of the skin.
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Affiliation(s)
- Nienke van der Stoep
- Division of Molecular Biology, Department of Immunohematology and Blood Transfusion, Building 1, E3-Q, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
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22
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Boss V, Sola A, Wen TC, Decker MJ. Mild Intermittent Hypoxia Does Not Induce Stress Responses in the Neonatal Rat Brain. Neonatology 2005; 88:313-20. [PMID: 16113526 DOI: 10.1159/000087629] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2005] [Accepted: 04/18/2005] [Indexed: 11/19/2022]
Abstract
We previously demonstrated that intermittent hypoxia evokes persistent changes in extracellular striatal dopamine, locomotor activity and executive function, using a rodent model emulating apnea of prematurity in which rat pups are exposed to 20-second bursts of hypoxic gas mix containing 10% oxygen (60 events/h; 6 h/day) from postnatal days 7 to 11. To determine whether subtle repetitive hypoxic insults also induce expression of stress-related genes, we employed real-time RT-PCR to assay gene transcription in neonatal rats subjected to the same paradigm. In addition, we also measured expression of stress-induced transcripts in an age-matched cohort following a more severe oxidative stressor: permanent focal ischemia. Four transcripts were elevated following the ischemic insult: heat shock protein 70 (Hsp70), CL100, nurr77, and heme oxygenase-1. In contrast, these transcripts were not regulated in the majority of neonatal rats exposed to an intermittent hypoxia protocol. Hsp70 was strongly induced, and CL100 and nurr77 were slightly induced in only 2 of 11 post-hypoxic rats compared to controls. These data demonstrate that a single ischemic event elicits expression of specific stress-related genes, whereas 5 days of brief intermittent hypoxic insults typically do not. Thus, it is unlikely that the neurochemical and behavioral morbidity observed in juvenile and adult rodents exposed to intermittent hypoxia during a critical period of brain development are related to stress-induced changes in gene expression.
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Affiliation(s)
- Valerie Boss
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA.
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23
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Abstract
Peptide loading of major histocompatibility class II molecules is catalyzed in late endosomal and lysosomal compartments of cells by the catalytic action of human leukocyte antigen (HLA)-DM (H-2M in mice). In B cells, dendritic cells and thymic epithelial cells, the peptide loading of class II molecules is modified by the expression of the non-classical class II molecule, HLA-DO (H-2O in mice). Collectively, studies to date support that DO/H-2O expression inhibits the presentation of antigens acquired by cells via fluid phase endocytosis. However, in B cells, the expression of H-2O promotes the presentation of antigens internalized by the B-cell receptor. In this review, we summarize the literature pertaining to DO assembly, transport, and function, with an emphasis on the function of DO/H-2O.
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Affiliation(s)
- Lisa K Denzin
- Sloan-Kettering Institute, Immunology Program, Memorial Sloan-Kettering Cancer Center, NY 10021, USA.
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24
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Abstract
The presentation of antigenic peptides by MHC class II molecules is essential for activation of CD4+ T cells. The formation of most peptide-MHC-class-II complexes is influenced by the actions of two specialized accessory proteins--DM and DO--located in the endosomal/lysosomal system where peptide loading occurs. DM removes class-II-associated invariant-chain peptide (CLIP) from newly synthesized class II molecules, but by now it is clearly established that this is only a special case of the general peptide-editing function of DM. Recent data have begun to explain the molecular basis for the editing activity. The other accessory protein, DO, modulates DM activity in vitro, but the physiological importance of DO is unclear. New evidence from several laboratories has provided clues that may soon change this.
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Affiliation(s)
- Lars Karlsson
- Johnson & Johnson Pharmaceutical Research and Development, 3210 Merryfield Row, San Diego, CA 92121, USA.
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25
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Abstract
HLA-DO (H2-O in mice) is a nonpolymorphic transmembrane alphabeta heterodimer encoded in the class II region of the major histocompatibility complex (MHC). It is expressed selectively in B lymphocytes and thymic medullary epithelial cells. DO forms a stable complex with the peptide-loading catalyst HLA-DM in the endoplasmic reticulum (ER); in the absence of DM, DO is unstable. During intracellular transport and distribution in the endosomal compartments, the ratio of DO to DM changes. In primary B cells, only approx 50% of DM molecules are associated with DO. DO appears to regulate the peptide-loading function of DM in the MHC class II antigen-presentation pathway. Although certain discrepancies are present, results from most studies indicate that DO (as well as H2-O) inhibits DM (H2-M) function; this inhibition is pH-dependent. As a consequence, DO restrains presentation of exogenous antigens delivered through nonreceptor-mediated mechanisms; in addition, DO alters the peptide repertoire that is associated with cell-surface class II molecules. The biological function of DO remains obscure, partially because of the lack of striking phenotypes in the H2-O knockout mice. Results from recent studies indicate that DO expression in B cells is dynamic, and highly regulated during B-cell development and B-cell activation, suggesting that the physiological role of DO is to tailor the antigen presentation function of the B-lineage cells to meet their primary function at each stage of B-cell development and maturation. Further investigations are needed in this direction.
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Affiliation(s)
- Xinjian Chen
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, 1639 Pierce Drive, Atlanta, GA 30322, USA.
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26
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van der Stoep N, Quinten E, Marcondes Rezende M, van den Elsen PJ. E47, IRF-4, and PU.1 synergize to induce B-cell-specific activation of the class II transactivator promoter III (CIITA-PIII). Blood 2004; 104:2849-57. [PMID: 15242870 DOI: 10.1182/blood-2004-03-0790] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AbstractIn B cells, expression of CIITA and resulting major histocompatibility complex II (MHCII) is mediated exclusively by promoter III (CIITA-PIII) activation. Recent studies have established that CIITA-PIII also participates in the expression of CIITA in activated human T cells, dendritic cells, and monocytes. In this study we characterized the various regulatory elements and interacting factors of CIITA-PIII that account for specific activation in B lymphocytes. We identified 2 E-box motifs and an Ets/ISRE-consensus element (EICE) in CIITA-PIII as playing a crucial role in the B-cell-specific transcriptional regulation of CIITA. Abolishment of factor binding to these elements resulted in a strong reduction of CIITA-PIII activation in B cells only, whereas it did scarcely affect or not affect the activity of CIITA-PIII in activated T cells and monocytes. We show that in B cells, E47 and PU.1/IRF-4 interact with the E-box motifs and the EICE, respectively, and act synergistically in the activation of CIITA-PIII. Moreover, functional inhibition of either E47 or IRF-4 resulted in strong reduction of CIITA-PIII activity in B lymphocytes only. The finding that PU.1, IRF-4, and E47 play an important role in the B-cell-mediated activation of CIITA-PIII provides a link between antigen presentation functions and activation and differentiation events in B lymphocytes.
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Affiliation(s)
- Nienke van der Stoep
- Division of Molecular Biology, Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, E3-Q, PO Box 9600, 2300 RC Leiden, the Netherlands.
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27
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Muhlethaler-Mottet A, Krawczyk M, Masternak K, Spilianakis C, Kretsovali A, Papamatheakis J, Reith W. The S Box of Major Histocompatibility Complex Class II Promoters Is a Key Determinant for Recruitment of the Transcriptional Co-activator CIITA. J Biol Chem 2004; 279:40529-35. [PMID: 15271997 DOI: 10.1074/jbc.m406585200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Tightly regulated expression of major histocompatibility complex (MHC) class II genes is critical for the immune system. A conserved regulatory module consisting of four cis-acting elements, the W, X, X2 and Y boxes, controls transcription of MHC class II genes. The X, X2, and Y boxes are bound, respectively, by RFX, CREB, and NF-Y to form a MHC class II-specific enhanceosome complex. The latter constitutes a landing pad for recruitment of the transcriptional co-activator CIITA. In contrast to the well defined roles of the X, X2, and Y boxes, the role of the W region has remained controversial. In vitro binding studies have suggested that it might contain a second RFX-binding site. We demonstrate here by means of promoter pull-down assays that the most conserved subsequence within the W region, called the S box, is a critical determinant for tethering of CIITA to the enhanceosome complex. Binding of CIITA to the enhanceosome requires both integrity of the S box and a remarkably stringent spacing between the S and X boxes. Even a 1-2-base pair change in the native S-X distance is detrimental for CIITA recruitment and promoter function. In contrast to current models, binding of RFX to a putative duplicated binding site in the W box is thus not required for either CIITA recruitment or promoter activity. This paves the way for the identification of novel factors mediating the contribution of the S box to the activation of MHC class II promoters.
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Affiliation(s)
- Annick Muhlethaler-Mottet
- University of Geneva Medical School, Department of Pathology and Immunology, Centre Médical Universitaire, 1 rue Michel-Servet, CH-1211, Geneva, Switzerland
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28
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Hornell TMC, Beresford GW, Bushey A, Boss JM, Mellins ED. Regulation of the class II MHC pathway in primary human monocytes by granulocyte-macrophage colony-stimulating factor. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2003; 171:2374-83. [PMID: 12928384 DOI: 10.4049/jimmunol.171.5.2374] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
GM-CSF stimulates the growth and differentiation of hematopoietic progenitors and also affects mature cell function. These effects have led to the use of GM-CSF as a vaccine adjuvant with promising results; however, the mechanisms underlying GM-CSF-mediated immune potentiation are incompletely understood. In this study, we investigated the hypothesis that the immune stimulatory role of GM-CSF is in part due to effects on class II MHC Ag presentation. We find that, in primary human monocytes treated for 24-48 h, GM-CSF increases surface class II MHC expression and decreases the relative level of the invariant chain-derived peptide, CLIP, bound to surface class II molecules. GM-CSF also increases expression of the costimulatory molecules CD86 and CD40, but not the differentiation marker CD1a or CD16. Furthermore, GM-CSF-treated monocytes are better stimulators in a mixed leukocyte reaction. Additional analyses of the class II pathway revealed that GM-CSF increases total protein and RNA levels of HLA-DR, DM, and DOalpha. Expression of class II transactivator (CIITA) types I and III, but not IV, transcripts increases in response to GM-CSF. Furthermore, GM-CSF increases the amount of CIITA associated with the DR promoter. Thus, our data argue that the proinflammatory role of GM-CSF is mediated in part through increased expression of key molecules involved in the class II MHC pathway via induction of CIITA.
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MESH Headings
- Adjuvants, Immunologic/pharmacology
- Antigen Presentation/immunology
- Antigens, CD/biosynthesis
- Antigens, Differentiation, B-Lymphocyte/biosynthesis
- Antigens, Differentiation, B-Lymphocyte/genetics
- Antigens, Differentiation, B-Lymphocyte/metabolism
- B7-2 Antigen
- CD40 Antigens/biosynthesis
- Cell Differentiation/immunology
- Cell Membrane/immunology
- Cell Membrane/metabolism
- Cells, Cultured
- Down-Regulation/genetics
- Down-Regulation/immunology
- Granulocyte-Macrophage Colony-Stimulating Factor/pharmacology
- HLA-D Antigens/biosynthesis
- HLA-D Antigens/genetics
- HLA-D Antigens/metabolism
- HLA-D Antigens/physiology
- HLA-DR Antigens/biosynthesis
- HLA-DR Antigens/genetics
- HLA-DR Antigens/metabolism
- HLA-DR alpha-Chains
- Histocompatibility Antigens Class II/biosynthesis
- Histocompatibility Antigens Class II/genetics
- Histocompatibility Antigens Class II/metabolism
- Humans
- Interferon-gamma/biosynthesis
- Interferon-gamma/pharmacology
- Interleukin-10/antagonists & inhibitors
- Interleukin-10/biosynthesis
- Membrane Glycoproteins/biosynthesis
- Monocytes/cytology
- Monocytes/immunology
- Monocytes/metabolism
- Promoter Regions, Genetic
- RNA, Messenger/biosynthesis
- Recombinant Proteins
- Signal Transduction/genetics
- Signal Transduction/immunology
- Transcription, Genetic/immunology
- Up-Regulation/genetics
- Up-Regulation/immunology
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Affiliation(s)
- Tara M C Hornell
- Department of Pediatrics, School of Medicine, Stanford University, CCSR Room 2120, 269 Campus Drive, Stanford, CA 94305, USA.
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Boekhoudt GH, Guo Z, Beresford GW, Boss JM. Communication between NF-kappa B and Sp1 controls histone acetylation within the proximal promoter of the monocyte chemoattractant protein 1 gene. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2003; 170:4139-47. [PMID: 12682245 DOI: 10.4049/jimmunol.170.8.4139] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The induction of the monocyte chemoattractant protein 1 gene (MCP-1) by TNF occurs through an NF-kappaB-dependent distal regulatory region and an Sp1-dependent proximal regulatory region that are separated by 2.2 kb of sequence. To investigate how these regions coordinate activation of MCP-1 in response to TNF, experiments were performed to examine the role of coactivators, changes in local chromatin structure, and the acetylation of histones at the MCP-1 regulatory regions. An E1a-sensitive coactivator was found to be required for expression. In vivo nuclease sensitivity assays identified changes in response to TNF at both the proximal and distal regions that were dependent on the p65 subunit of NF-kappaB and Sp1. Chromatin immunoprecipitations used to analyze factor assembly and histone acetylation at the distal and proximal regions showed that Sp1 binding to and histone acetylation of the proximal region was dependent on NF-kappaB p65. Conversely, Sp1 assembly at the proximal region was required for p65 binding to and acetylation of the distal region, suggesting communication between the two regions during gene activation. These data and the NF-kappaB p65-dependent histone acetylation of a middle region sequence suggest a potential order for the assembly, acetylation and accessibility of the MCP-1 regulatory regions in response to TNF.
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Affiliation(s)
- Gunther H Boekhoudt
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
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Khalil H, Deshaies F, Bellemare-Pelletier A, Brunet A, Faubert A, Azar GA, Thibodeau J. Class II transactivator-induced expression of HLA-DO(beta) in HeLa cells. TISSUE ANTIGENS 2002; 60:372-82. [PMID: 12492813 DOI: 10.1034/j.1399-0039.2002.600504.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
HLA-DO is an intracellular nonclassical MHC class II molecule expressed in the endocytic pathway of B lymphocytes. It shapes the repertoire of peptides bound to classical class II molecules such as HLA-DR by regulating the activity of HLA-DM. Using a peptide corresponding to the cytoplasmic tail of HLA-DO(beta), we have developed a mouse monoclonal antibody, HKC5. Immunofluorescence microscopy revealed that HKC5 recognizes HLA-DO molecules present in the endoplasmic reticulum as well as those in vesicular compartments of the endocytic pathway. In addition, the antibody detects the isolated beta chain on Western blots. Using mutants of the DO(beta) cytoplasmic tail fused to a reporter molecule and expressed in epithelial cells, we showed by flow cytometry that the antibody epitope includes one or both of the leucine residues forming the lysosomal sorting signal. Finally, we have used HKC5 to evaluate the presence of the HLA-DO(beta) chain in HeLa cells expressing the class II transactivator protein CIITA. Our flow cytometry and confocal microscopy analyses showed a marked expression of DO(beta) suggesting that HLA-DO could accumulate under the influence of CIITA in non-B cells.
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Affiliation(s)
- H Khalil
- Laboratoire d'Immunologie Moléculaire, Département de Microbiologie et Immunologie, Faculté de Médecine, Université de Montréal, Québec, Canada
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Nagarajan UM, Bushey A, Boss JM. Modulation of gene expression by the MHC class II transactivator. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2002; 169:5078-88. [PMID: 12391224 DOI: 10.4049/jimmunol.169.9.5078] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The class II transactivator (CIITA) is a master regulator of MHC class II expression. CIITA also modulates the expression of MHC class I genes, suggesting that it may have a more global role in gene expression. To determine whether CIITA regulates genes other than the MHC class II and I family, DNA microarray analysis was used to compare the expression profiles of the CIITA expressing B cell line Raji and its CIITA-negative counterpart RJ2.2.5. The comparison identified a wide variety of genes whose expression was modulated by CIITA. Real time RT-PCR from Raji, RJ2.2.5, an RJ2.2.5 cell line complemented with CIITA, was performed to confirm the results and to further identify CIITA-regulated genes. CIITA-regulated genes were found to have diverse functions, which could impact Ag processing, signaling, and proliferation. Of note was the identification of a set of genes localized to chromosome 1p34-35. The global modulation of genes in a local region suggests that this region may share some regulatory control with the MHC.
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Affiliation(s)
- Uma M Nagarajan
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
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Abstract
The presentation of peptides to T cells by MHC class II molecules is of critical importance in specific recognition by the immune system. Expression of class II molecules is exquisitely controlled at the transcriptional level. A large set of proteins interact with the promoters of class II genes. The most important of these is CIITA, a master controller that orchestrates expression but does not bind directly to the promoter. The transcriptosome complex formed at class II promoters is a model for induction of gene expression.
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Affiliation(s)
- Jenny Pan-Yun Ting
- Department of Microbiology and Immunology and The Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.
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