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Yates J, Schaufelberger H, Steinacher R, Schär P, Truninger K, Boeva V. DNA-methylation variability in normal mucosa: a field cancerization marker in patients with adenomatous polyps. J Natl Cancer Inst 2024; 116:974-982. [PMID: 38273663 PMCID: PMC11160500 DOI: 10.1093/jnci/djae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/13/2023] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND The phenomenon of field cancerization reflects the transition of normal cells into those predisposed to cancer. Assessing the scope and intensity of this process in the colon may support risk prediction and colorectal cancer prevention. METHODS The Swiss Epigenetic Colorectal Cancer Study (SWEPIC) study, encompassing 1111 participants for DNA methylation analysis and a subset of 84 for RNA sequencing, was employed to detect field cancerization in individuals with adenomatous polyps (AP). Methylation variations were evaluated for their discriminative capability, including in external cohorts, genomic localization, clinical correlations, and associated RNA expression patterns. RESULTS Normal cecal tissue of individuals harboring an AP in the proximal colon manifested dysregulated DNA methylation compared to tissue from healthy individuals at 558 unique loci. Leveraging these adenoma-related differentially variable and methylated CpGs (aDVMCs), our classifier discerned between healthy and AP-adjacent tissues across SWEPIC datasets (cross-validated area under the receiver operating characteristic curve [ROC AUC] = 0.63-0.81), including within age-stratified cohorts. This discriminative capacity was validated in 3 external sets, differentiating healthy from cancer-adjacent tissue (ROC AUC = 0.82-0.88). Notably, aDVMC dysregulation correlated with polyp multiplicity. More than 50% of aDVMCs were significantly associated with age. These aDVMCs were enriched in active regions of the genome (P < .001), and associated genes exhibited altered expression in AP-adjacent tissues. CONCLUSIONS Our findings underscore the early onset of field cancerization in the right colon during the neoplastic transformation process. A more extensive validation of aDVMC dysregulation as a stratification tool could pave the way for enhanced surveillance approaches, especially given its linkage to adenoma emergence.
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Affiliation(s)
- Josephine Yates
- Department of Computer Science, Institute for Machine Learning, ETH Zürich, Zurich, Switzerland
- ETH AI Center, ETH Zürich, Zurich, Switzerland
- Swiss Institute for Bioinformatics (SIB), Lausanne, Switzerland
| | | | | | - Primo Schär
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Kaspar Truninger
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
| | - Valentina Boeva
- Department of Computer Science, Institute for Machine Learning, ETH Zürich, Zurich, Switzerland
- ETH AI Center, ETH Zürich, Zurich, Switzerland
- Swiss Institute for Bioinformatics (SIB), Lausanne, Switzerland
- Cochin Institute, Inserm U1016, National Centre for Scientific Research (CNRS) UMR 8104, Paris Descartes University UMR-S1016, Paris, France
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2
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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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3
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Văcăraş V, Vulturar R, Chiş A, Damian L. Inclusion body myositis, viral infections, and TDP-43: a narrative review. Clin Exp Med 2024; 24:91. [PMID: 38693436 PMCID: PMC11062973 DOI: 10.1007/s10238-024-01353-9] [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: 03/21/2024] [Accepted: 04/15/2024] [Indexed: 05/03/2024]
Abstract
The ubiquitous RNA-processing molecule TDP-43 is involved in neuromuscular diseases such as inclusion body myositis, a late-onset acquired inflammatory myopathy. TDP-43 solubility and function are disrupted in certain viral infections. Certain viruses, high viremia, co-infections, reactivation of latent viruses, and post-acute expansion of cytotoxic T cells may all contribute to inclusion body myositis, mainly in an age-shaped immune landscape. The virally induced senescent, interferon gamma-producing cytotoxic CD8+ T cells with increased inflammatory, and cytotoxic features are involved in the occurrence of inclusion body myositis in most such cases, in a genetically predisposed host. We discuss the putative mechanisms linking inclusion body myositis, TDP-43, and viral infections untangling the links between viruses, interferon, and neuromuscular degeneration could shed a light on the pathogenesis of the inclusion body myositis and other TDP-43-related neuromuscular diseases, with possible therapeutic implications.
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Affiliation(s)
- Vitalie Văcăraş
- Department of Neurosciences, "Iuliu Haţieganu" University of Medicine and Pharmacy, Cluj-Napoca, 43, Victor Babeş St, 400012, Cluj-Napoca, Romania
- Neurology Department of Cluj, County Emergency Hospital, 3-5, Clinicilor St, 400347, Cluj-Napoca, Romania
| | - Romana Vulturar
- Department of Molecular Sciences, "Iuliu Haţieganu" University of Medicine and Pharmacy Cluj-Napoca, 6, Pasteur St, 400349, Cluj-Napoca, Romania
- Cognitive Neuroscience Laboratory, University Babeş-Bolyai, 30, Fântânele St, 400294, Cluj-Napoca, Romania
- Association for Innovation in Rare Inflammatory, Metabolic, Genetic Diseases INNOROG, 30E, Făgetului St, 400497, Cluj-Napoca, Romania
| | - Adina Chiş
- Department of Molecular Sciences, "Iuliu Haţieganu" University of Medicine and Pharmacy Cluj-Napoca, 6, Pasteur St, 400349, Cluj-Napoca, Romania.
- Cognitive Neuroscience Laboratory, University Babeş-Bolyai, 30, Fântânele St, 400294, Cluj-Napoca, Romania.
- Association for Innovation in Rare Inflammatory, Metabolic, Genetic Diseases INNOROG, 30E, Făgetului St, 400497, Cluj-Napoca, Romania.
| | - Laura Damian
- Association for Innovation in Rare Inflammatory, Metabolic, Genetic Diseases INNOROG, 30E, Făgetului St, 400497, Cluj-Napoca, Romania
- Department of Rheumatology, Centre for Rare Autoimmune and Autoinflammatory Diseases, Emergency, Clinical County Hospital Cluj, 2-4, Clinicilor St, 400006, Cluj-Napoca, Romania
- CMI Reumatologie Dr. Damian, 6-8, Petru Maior St, 400002, Cluj-Napoca, Romania
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4
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Seo J, Gaddis NC, Patchen BK, Xu J, Barr RG, O'Connor G, Manichaikul AW, Gharib SA, Dupuis J, North KE, Cassano PA, Hancock DB. Exploiting meta-analysis of genome-wide interaction with serum 25-hydroxyvitamin D to identify novel genetic loci associated with pulmonary function. Am J Clin Nutr 2024; 119:1227-1237. [PMID: 38484975 PMCID: PMC11130669 DOI: 10.1016/j.ajcnut.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 02/12/2024] [Accepted: 03/07/2024] [Indexed: 04/01/2024] Open
Abstract
BACKGROUND Higher 25-hydroxyvitamin D (25(OH)D) concentrations in serum has a positive association with pulmonary function. Investigating genome-wide interactions with 25(OH)D may reveal new biological insights into pulmonary function. OBJECTIVES We aimed to identify novel genetic variants associated with pulmonary function by accounting for 25(OH)D interactions. METHODS We included 211,264 participants from the observational United Kingdom Biobank study with pulmonary function tests (PFTs), genome-wide genotypes, and 25(OH)D concentrations from 4 ancestral backgrounds-European, African, East Asian, and South Asian. Among PFTs, we focused on forced expiratory volume in the first second (FEV1) and forced vital capacity (FVC) because both were previously associated with 25(OH)D. We performed genome-wide association study (GWAS) analyses that accounted for variant×25(OH)D interaction using the joint 2 degree-of-freedom (2df) method, stratified by participants' smoking history and ancestry, and meta-analyzed results. We evaluated interaction effects to determine how variant-PFT associations were modified by 25(OH)D concentrations and conducted pathway enrichment analysis to examine the biological relevance of our findings. RESULTS Our GWAS meta-analyses, accounting for interaction with 25(OH)D, revealed 30 genetic variants significantly associated with FEV1 or FVC (P2df <5.00×10-8) that were not previously reported for PFT-related traits. These novel variant signals were enriched in lung function-relevant pathways, including the p38 MAPK pathway. Among variants with genome-wide-significant 2df results, smoking-stratified meta-analyses identified 5 variants with 25(OH)D interactions that influenced FEV1 in both smoking groups (never smokers P1df interaction<2.65×10-4; ever smokers P1df interaction<1.71×10-5); rs3130553, rs2894186, rs79277477, and rs3130929 associations were only evident in never smokers, and the rs4678408 association was only found in ever smokers. CONCLUSION Genetic variant associations with lung function can be modified by 25(OH)D, and smoking history can further modify variant×25(OH)D interactions. These results expand the known genetic architecture of pulmonary function and add evidence that gene-environment interactions, including with 25(OH)D and smoking, influence lung function.
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Affiliation(s)
- Jungkyun Seo
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, United States
| | - Nathan C Gaddis
- RTI International, Research Triangle Park, NC, United States
| | - Bonnie K Patchen
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, United States
| | - Jiayi Xu
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, United States
| | - R Graham Barr
- Divisions of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Medical Center, New York, NY, United States
| | - George O'Connor
- Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Ani W Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Sina A Gharib
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, United States; Division of Pulmonary, Critical Care and Sleep Medicine, Computational Medicine Core, Center for Lung Biology, University of Washington, Seattle, WA, United States
| | - Josée Dupuis
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Kari E North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, United States
| | - Patricia A Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, United States; Division of Epidemiology, Department of Population Health Sciences, Weill Cornell Medicine, NY, United States
| | - Dana B Hancock
- RTI International, Research Triangle Park, NC, United States.
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Li Q, Zhang L, Zou H, Chai T, Su Y, Shen Y, He X, Qi H, Li C. Multi-omics reveals the switch role of abnormal methylation in the regulation of decidual macrophages function in recurrent spontaneous abortion. Cell Signal 2024; 117:111071. [PMID: 38295895 DOI: 10.1016/j.cellsig.2024.111071] [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: 11/05/2023] [Revised: 01/09/2024] [Accepted: 01/28/2024] [Indexed: 02/05/2024]
Abstract
RSA, recurrent spontaneous abortion, often causes serious physical damage and psychological pressure in reproductive women with unclarified pathogenesis. Abnormal function of decidual cells and aberrant DNA methylation have been reported to cause RSA, but their association remains unclear. Here, we integrated transcriptome, DNA methylome, and scRNA-seq to clarify the regulatory relationship between DNA methylation and decidual cells in RSA. We found that DNA methylation mainly influenced the function of decidual macrophages (DMs), of which four hub genes, HLA-A, HLA-F, SQSTM1/P62, and Interferon regulatory factor 7 (IRF7), related to 22 hypomethylated CpG sites, regulated 16 hub pathways to participate in RSA pathogenesis. In particular, using transcription factor analysis, it is suggested that the upregulation of IRF7 transcription was associated with enhanced recruitment of the transcription factor STAT1 by the hypomethylated promoter region of IRF7. As the current research on DNA methylation of macrophages in the uterine microenvironment of RSA is still blank, our systematic picture of abnormal DNA methylation in regulating DM function provides new insights into the role of DNA methylation in RSA occurrence, which may aid in further prevention and treatment of RSA.
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Affiliation(s)
- Qian Li
- Department of Clinical Laboratory, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Department of Clinical Laboratory, Chongqing Health Center for Women and Children, Chongqing, China
| | - Lei Zhang
- Department of Clinical Laboratory, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Department of Clinical Laboratory, Chongqing Health Center for Women and Children, Chongqing, China
| | - Hua Zou
- Department of Clinical Laboratory, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Department of Clinical Laboratory, Chongqing Health Center for Women and Children, Chongqing, China
| | - Tingjia Chai
- Department of Endocrine Laboratory, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yan Su
- Department of Clinical Laboratory, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Department of Clinical Laboratory, Chongqing Health Center for Women and Children, Chongqing, China
| | - Yan Shen
- Department of Clinical Laboratory, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Department of Clinical Laboratory, Chongqing Health Center for Women and Children, Chongqing, China
| | - Xiao He
- Department of Clinical Laboratory, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Department of Clinical Laboratory, Chongqing Health Center for Women and Children, Chongqing, China
| | - Hongbo Qi
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, China; Department of Obstetrics and Gynecology, Chongqing Health Center for Women and Children, China.
| | - Chunli Li
- Department of Clinical Laboratory, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Department of Clinical Laboratory, Chongqing Health Center for Women and Children, Chongqing, China.
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6
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Vasoya D, Connelley T, Tzelos T, Todd H, Ballingall KT. Large scale transcriptional analysis of MHC class I haplotype diversity in sheep. HLA 2024; 103:e15356. [PMID: 38304958 DOI: 10.1111/tan.15356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/15/2023] [Accepted: 01/09/2024] [Indexed: 02/03/2024]
Abstract
Domestic sheep (Ovis aries) have been an important component of livestock agricultural production for thousands of years. Preserving genetic diversity within livestock populations maintains a capacity to respond to changing environments and rapidly evolving pathogens. MHC genetic diversity can influence immune functionality at individual and population levels. Here, we focus on defining functional MHC class I haplotype diversity in a large cohort of Scottish Blackface sheep pre-selected for high levels of MHC class II DRB1 diversity. Using high-throughput amplicon sequencing with three independent sets of barcoded primers we identified 134 MHC class I transcripts within 38 haplotypes. Haplotypes were identified with between two and six MHC class I genes, plus variable numbers of conserved sequences with very low read frequencies. One or two highly transcribed transcripts dominate each haplotype indicative of two highly polymorphic, classical MHC class I genes. Additional clusters of medium, low, and very low expressed transcripts are described, indicative of lower transcribed classical, non-classical and genes whose function remains to be determined.
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Affiliation(s)
- Deepali Vasoya
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Scotland, UK
| | - Timothy Connelley
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Scotland, UK
| | - Thomas Tzelos
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Scotland, UK
- Moredun Research Institute, Pentlands Science Park, Scotland, UK
| | - Helen Todd
- Moredun Research Institute, Pentlands Science Park, Scotland, UK
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Sverchkova A, Burkholz S, Rubsamen R, Stratford R, Clancy T. Integrative HLA typing of tumor and adjacent normal tissue can reveal insights into the tumor immune response. BMC Med Genomics 2024; 17:37. [PMID: 38281021 PMCID: PMC10821267 DOI: 10.1186/s12920-024-01808-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 01/12/2024] [Indexed: 01/29/2024] Open
Abstract
BACKGROUND The HLA complex is the most polymorphic region of the human genome, and its improved characterization can help us understand the genetics of human disease as well as the interplay between cancer and the immune system. The main function of HLA genes is to recognize "non-self" antigens and to present them on the cell surface to T cells, which instigate an immune response toward infected or transformed cells. While sequence variation in the antigen-binding groove of HLA may modulate the repertoire of immunogenic antigens presented to T cells, alterations in HLA expression can significantly influence the immune response to pathogens and cancer. METHODS RNA sequencing was used here to accurately genotype the HLA region and quantify and compare the level of allele-specific HLA expression in tumors and patient-matched adjacent normal tissue. The computational approach utilized in the study types classical and non-classical Class I and Class II HLA alleles from RNA-seq while simultaneously quantifying allele-specific or personalized HLA expression. The strategy also uses RNA-seq data to infer immune cell infiltration into tumors and the corresponding immune cell composition of matched normal tissue, to reveal potential insights related to T cell and NK cell interactions with tumor HLA alleles. RESULTS The genotyping method outperforms existing RNA-seq-based HLA typing tools for Class II HLA genotyping. Further, we demonstrate its potential for studying tumor-immune interactions by applying the method to tumor samples from two different subtypes of breast cancer and their matched normal breast tissue controls. CONCLUSIONS The integrative RNA-seq-based HLA typing approach described in the study, coupled with HLA expression analysis, neoantigen prediction and immune cell infiltration, may help increase our understanding of the interplay between a patient's tumor and immune system; and provide further insights into the immune mechanisms that determine a positive or negative outcome following treatment with immunotherapy such as checkpoint blockade.
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Affiliation(s)
- Angelina Sverchkova
- NEC OncoImmunity, Oslo Cancer Cluster, Innovation Park, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Scott Burkholz
- Flow Pharma, Inc, Warrensville Heights, Galaxy Parkway, OH, 4829, USA
| | - Reid Rubsamen
- Flow Pharma, Inc, Warrensville Heights, Galaxy Parkway, OH, 4829, USA
- University Hospitals, Cleveland Medical Center, Cleveland, OH, USA
- Case Western Reserve School of Medicine, Cleveland, OH, USA
| | - Richard Stratford
- NEC OncoImmunity, Oslo Cancer Cluster, Innovation Park, Oslo, Norway
| | - Trevor Clancy
- NEC OncoImmunity, Oslo Cancer Cluster, Innovation Park, Oslo, Norway.
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Lin Y, Tang H, Teng H, Feng W, Li F, Liu S, Liu Y, Wei Q. Development and validation of neutrophil extracellular traps-derived signature to predict the prognosis for osteosarcoma patients. Int Immunopharmacol 2024; 127:111364. [PMID: 38101221 DOI: 10.1016/j.intimp.2023.111364] [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: 05/09/2023] [Revised: 11/18/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023]
Abstract
Neutrophil extracellular traps (NETs) have been reported to be crucial in tumorigenesis and malignant progression. However, their prognostic significance, association with tumor immune microenvironment (TIME), and therapeutic response in osteosarcoma (OS) stills remain unclear. Hence, TARGET and GSE21257 cohorts were included for analysis. Single-sample gene set enrichment analysis (ssGSEA) and weighted gene co-expression network analysis (WGCNA) were conducted to extract NETs-derived genes. Subsequently, the NETs score (NETScore) model, consisting of 4 signature genes, was established and validated with the least absolute shrinkage and selection operator (LASSO) and Cox regression analysis. Our results indicated that NETScore has satisfactory predictability of the patient's overall survival, with AUC values at 1-, 3- and 5-year in the training cohort of 0.798, 0.792 and 0.804, respectively; similar prominent prediction performance was obtained in three validation cohorts. Further, real-time quantitative PCR (RT-qPCR) assay was conducted to determine the expression of signature genes in human osteoblasts and OS cells. Besides, NETScore and clinical factors (age, gender, metastatic status) were integrated to construct a nomogram. C-index and AUC values at 1-, 3-, and 5-year were above 0.800, displaying robust predictive performance. Patients with high and low NETScore had different immune statuses and drug sensitivity. Meanwhile, several positive regulatory immune function pathways, including T cell proliferation, activation and migration, were significantly suppressed among patients with high NETScore. Summarily, we established a novel NETScore that can accurately predict OS patients' prognosis, which correlated closely with the immune landscape and therapeutic response and might help to guide clinical decision-making.
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Affiliation(s)
- Yunhua Lin
- Department of Trauma Orthopedic and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Haijun Tang
- Department of Spine and Osteopathic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Hongcai Teng
- Department of Spine and Osteopathic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Wenyu Feng
- Department of Orthopedics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Feicui Li
- Department of Spine and Osteopathic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Shangyu Liu
- Department of Spine and Osteopathic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yun Liu
- Department of Spine and Osteopathic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.
| | - Qingjun Wei
- Department of Trauma Orthopedic and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.
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9
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Lee DH, Imran M, Choi JH, Park YJ, Kim YH, Min S, Park TJ, Choi YW. CDK4/6 inhibitors induce breast cancer senescence with enhanced anti-tumor immunogenic properties compared with DNA-damaging agents. Mol Oncol 2024; 18:216-232. [PMID: 37854019 PMCID: PMC10766199 DOI: 10.1002/1878-0261.13541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 10/05/2023] [Accepted: 10/17/2023] [Indexed: 10/20/2023] Open
Abstract
Since therapy-induced senescence (TIS) can either support or inhibit cancer progression, identifying which types of chemotherapeutic agents can produce the strongest anti-tumor TIS is an important issue. Here, cyclin-dependent kinase4/6 inhibitors (CDK4/6i)-induced senescence was compared to the TIS induced by conventional DNA-damaging agents. Despite both types of agents eliciting a similar degree of senescence, we observed increased expression of the senescence-associated secretory phenotype (SASP) and ligands related to pro-tumor immunity (IL6, CXCL8, TGFβ, CD274, and CEACAM1) and angiogenesis (VEGFA) mainly in TIS induced by DNA-damaging agents rather than by CDK4/6i. Additionally, although all agents increased the expression of anti-tumor immunomodulatory proteins related to antigen presentation (MHC-I, B2M) and T cell chemokines (CXCL9, 10, 11), CDK4/6i-induced senescent cells still maintained this expression at a similar or even higher intensity than cells treated with DNA-damaging agents, despite the absence of nuclear factor-kappa-B (NF-κB) and p53 activation. These data suggest that in contrast with DNA-damaging agents, which augment the pro-tumorigenic microenvironment via pro-inflammatory SASP, CDK4/6i can generate TIS only with antitumor immunomodulatory proteins.
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Affiliation(s)
- Dong Hyun Lee
- Department of Biochemistry and Molecular BiologyAjou University School of MedicineSuwonKorea
- Department of Biomedical SciencesAjou University Graduate School of MedicineSuwonKorea
- Inflamm‐Aging Translational Research CenterAjou University Medical CenterSuwonKorea
| | - Muhammad Imran
- Department of Biochemistry and Molecular BiologyAjou University School of MedicineSuwonKorea
- Inflamm‐Aging Translational Research CenterAjou University Medical CenterSuwonKorea
| | - Jae Ho Choi
- Inflamm‐Aging Translational Research CenterAjou University Medical CenterSuwonKorea
- Department of Hematology‐OncologyAjou University School of MedicineSuwonKorea
| | - Yoo Jung Park
- Department of Hematology‐OncologyAjou University School of MedicineSuwonKorea
| | - Young Hwa Kim
- Inflamm‐Aging Translational Research CenterAjou University Medical CenterSuwonKorea
| | - Sunwoo Min
- Department of Biological SciencesKorea Advanced Institute of Science and Technology (KAIST)DaejeonKorea
| | - Tae Jun Park
- Department of Biochemistry and Molecular BiologyAjou University School of MedicineSuwonKorea
- Department of Biomedical SciencesAjou University Graduate School of MedicineSuwonKorea
- Inflamm‐Aging Translational Research CenterAjou University Medical CenterSuwonKorea
| | - Yong Won Choi
- Inflamm‐Aging Translational Research CenterAjou University Medical CenterSuwonKorea
- Department of Hematology‐OncologyAjou University School of MedicineSuwonKorea
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10
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Shariatmadar Taleghani A, Zohrab Beigi Y, Zare-Mirakabad F, Masoudi-Nejad A. Exploring ceRNA networks for key biomarkers in breast cancer subtypes and immune regulation. Sci Rep 2023; 13:20795. [PMID: 38012271 PMCID: PMC10682442 DOI: 10.1038/s41598-023-47816-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 11/18/2023] [Indexed: 11/29/2023] Open
Abstract
Breast cancer is a major global health concern, and recent researches have highlighted the critical roles of non-coding RNAs in both cancer and the immune system. The competing endogenous RNA hypothesis suggests that various types of RNA, including coding and non-coding RNAs, compete for microRNA targets, acting as molecular sponges. This study introduces the Pre_CLM_BCS pipeline to investigate the potential of long non-coding RNAs and circular RNAs as biomarkers in breast cancer subtypes. The pipeline identifies specific modules within each subtype that contain at least one long non-coding RNA or circular RNA exhibiting significantly distinct expression patterns when compared to other subtypes. The results reveal potential biomarker genes for each subtype, such as circ_001845, circ_001124, circ_003925, circ_000736, and circ_003996 for the basal-like subtype, circ_00306 and circ_00128 for the luminal B subtype, circ_000709 and NPHS1 for the normal-like subtype, CAMKV and circ_001855 for the luminal A subtype, and circ_00128 and circ_00173 for the HER2+ subtype. Additionally, certain long non-coding RNAs and circular RNAs, including RGS5-AS1, C6orf223, HHLA3-AS1, circ_000349, circ_003996, circ_003925, circ_002665, circ_001855, and DLEU1, are identified as potential regulators of T cell mechanisms, underscoring their importance in understanding breast cancer progression in various subtypes. This pipeline provides valuable insights into cancer and immune-related processes in breast cancer subtypes.
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Affiliation(s)
- Alireza Shariatmadar Taleghani
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Yasaman Zohrab Beigi
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Fatemeh Zare-Mirakabad
- Department of Mathematics and Computer Science, Amirkabir University of Technology (Polytechnic Tehran), Tehran, Iran.
| | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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Huang L, Tu Z, Wei L, Sun W, Wang Y, Bi S, He F, Du L, Chen J, Kzhyshkowska J, Wang H, Chen D, Zhang S. Generating Functional Multicellular Organoids from Human Placenta Villi. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301565. [PMID: 37438660 PMCID: PMC10502861 DOI: 10.1002/advs.202301565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/26/2023] [Indexed: 07/14/2023]
Abstract
The interaction between trophoblasts, stroma cells, and immune cells at the maternal-fetal interface constitutes the functional units of the placenta, which is crucial for successful pregnancy outcomes. However, the investigation of this intricate interplay is restricted due to the absence of efficient experimental models. To address this challenge, a robust, reliable methodology for generating placenta villi organoids (PVOs) from early, late, or diseased pregnancies using air-liquid surface culture is developed. PVOs contain cytotrophoblasts that can self-renew and differentiate directly, along with stromal elements that retain native immune cells. Analysis of scRNA sequencing and WES data reveals that PVOs faithfully recapitulate the cellular components and genetic alterations of the corresponding source tissue. Additionally, PVOs derived from patients with preeclampsia exhibit specific pathological features such as inflammation, antiangiogenic imbalance, and decreased syncytin expression. The PVO-based propagation of primary placenta villi should enable a deeper investigation of placenta development and exploration of the underlying pathogenesis and therapeutics of placenta-originated diseases.
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Affiliation(s)
- Lijun Huang
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510150China
| | - Zhaowei Tu
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510150China
| | - Liudan Wei
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510150China
| | - Wei Sun
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510150China
| | - Yifan Wang
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510150China
| | - Shilei Bi
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510150China
| | - Fang He
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510150China
| | - Lili Du
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510150China
| | - Jingsi Chen
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510150China
| | - Julia Kzhyshkowska
- Institute of Transfusion Medicine and ImmunologyMedical Faculty MannheimUniversity of Heidelberg68167MannheimGermany
| | - Haibin Wang
- Fujian Provincial Key Laboratory of Reproductive Health ResearchDepartment of Obstetrics and GynecologyThe First Affiliated Hospital of Xiamen UniversitySchool of MedicineXiamen UniversityXiamen361005China
| | - Dunjin Chen
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510150China
- Key Laboratory for Major Obstetric Diseases of Guangdong ProvinceGuangzhou510150China
- Guangdong‐Hong Kong‐Macao Greater Bay Area Higher Education Joint Laboratory of Maternal‐Fetal MedicineGuangzhou510150China
- Guangdong Engineering and Technology Research Center of Maternal‐Fetal MedicineGuangzhou510150China
| | - Shuang Zhang
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510150China
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Ormandjieva A, Yordanov S, Stoyanov H, Deliverska E, Shivarov V, Ivanova M. The role of non-classical and chain-related human leukocyte antigen polymorphisms in laryngeal squamous cell carcinoma. Mol Biol Rep 2023; 50:7245-7252. [PMID: 37418079 DOI: 10.1007/s11033-023-08629-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/23/2023] [Indexed: 07/08/2023]
Abstract
BACKGROUND Laryngeal squamous cell carcinoma (LSCC) is the major pathological subtype of laryngeal cancer. It has been shown that alterations of the expression of non-classical human leukocyte antigens (HLA) and the chain-related MIC molecules by malignant cells can lead to escape from the immune system control and certain allele variants may participate in immune editing and therefore be associated with modulation of cancer risk. The aim of the present study was to investigate the role of non-classical HLA class Ib and chain-related MIC polymorphisms, determined at the allelic level by next-generation sequencing (NGS), in patients from the Bulgarian population, diagnosed with LSCC. MATERIALS AND METHODS In the present study DNA samples from 48 patients with LSCC were used. Data was compared to 63 healthy controls analysed in previous studies. HLA genotyping was performed by using the AlloSeq Tx17 early pooling protocol and the library preparation AlloSeq Tx17 kit (CareDx). Sequencing was performed on MiniSeq sequencing platform (Illumina) and HLA genotypes were assigned with the AlloSeq Assign analysis software v1.0.3 (CareDx) and the IPD-IMGT/HLA database 3.45.1.2. RESULTS The HLA disease association tests revealed a statistically significant predisposing association of HLA-F*01:01:02 (Pc = 0.0103, OR = 24.0194) with LSCC, while HLA-F*01:01:01 (Pc = 8.21e-04, OR = 0.0485) has a possible protective association. Additionally we observed several haplotypes with statistically significant protective and predisposing associations. The strongest association was observed for F*01:01:01-H*01:01:01 (P = 0.0054, haplotype score=-2.7801). CONCLUSION Our preliminary study suggests the involvement of HLA class Ib in cancer development and the possible role of the shown alleles as biomarkers of LSCC.
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Affiliation(s)
- Anastasia Ormandjieva
- Department of Clinical Immunology, Medical Faculty, Medical University, Sofia, Bulgaria.
| | | | - Hristo Stoyanov
- Department of Dental, Oral and Maxillofacial surgery, FDM, Medical University - Sofia, Sofia, Bulgaria
| | - Elitsa Deliverska
- Department of Dental, Oral and Maxillofacial surgery, FDM, Medical University - Sofia, Sofia, Bulgaria
| | - Velizar Shivarov
- Department of Experimental Research, Medical University Pleven, Pleven, Bulgaria
| | - Milena Ivanova
- Department of Clinical Immunology, Medical Faculty, Medical University, Sofia, Bulgaria
- Clinic of Clinical Immunology with Stem Cell Bank, University Hospital ''Alexandrovska'', Sofia, Bulgaria
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Neeson PJ, Ekert PG. Harnessing immune checkpoint trial data in pediatric cancer. NATURE CANCER 2023; 4:444-446. [PMID: 37106113 DOI: 10.1038/s43018-023-00540-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Affiliation(s)
- Paul J Neeson
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia.
| | - Paul G Ekert
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia.
- Murdoch Children's Research Institute, Parkville, Victoria, Australia.
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, Australia.
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia.
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Identification of potential tumor antigens and immune subtypes for lung adenocarcinoma. Med Oncol 2023; 40:100. [PMID: 36809467 DOI: 10.1007/s12032-023-01973-3] [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: 12/30/2022] [Accepted: 02/05/2023] [Indexed: 02/23/2023]
Abstract
In lung adenocarcinoma (LUAD), tumor antigens and immune phenotypes are important for cancer immunotherapy. This study aims to identify potential tumor antigens and immune subtypes for LUAD. In this study, the gene expression profiles and related clinical data of LUAD patients were collected from the TCGA and the GEO database. Then, we first identified four genes with copy number variation and mutation related to the survival of LUAD patients, in which FAM117A, INPP5J, and SLC25A42 were screened as potential tumor antigens. The expressions of these genes were significantly correlated with the infiltration of B cells CD4+ T cells and dendritic cells using TIMER and CIBERSORT algorithms. LUAD patients were divided into three immune clusters: C1(immune-desert), C2(immune-active), and C3(inflamed) using the Non-negative matrix factorization algorithm by using survival-related immune genes. The C2 cluster showed favorable overall survival compared to C1 and C3 clusters in both TCGA and two GEO LUAD cohorts. Different immune cell infiltration patterns, immune-associated molecular characteristics, and drug sensitivity were found among the three clusters. Moreover, different positions in the immune landscape map exhibited different prognostic characteristics using dimensionality reduction, providing further evidence of the immune clusters. The Weighted Gene Co-Expression Network Analysis was used to identify the co-expression modules of these immune genes. the three subtypes were significantly positively correlated with the turquoise module gene list, indicating a good prognosis with high scores. We hope that the identified tumor antigens and immune subtypes can be used for immunotherapy and prognosis in LUAD patients.
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Nakayama M, Marchi H, Dmitrieva AM, Chakraborty A, Merl-Pham J, Hennen E, Le Gleut R, Ruppert C, Guenther A, Kahnert K, Behr J, Hilgendorff A, Hauck SM, Adler H, Staab-Weijnitz CA. Quantitative proteomics of differentiated primary bronchial epithelial cells from chronic obstructive pulmonary disease and control identifies potential novel host factors post-influenza A virus infection. Front Microbiol 2023; 13:957830. [PMID: 36713229 PMCID: PMC9875134 DOI: 10.3389/fmicb.2022.957830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023] Open
Abstract
Background Chronic obstructive pulmonary disease (COPD) collectively refers to chronic and progressive lung diseases that cause irreversible limitations in airflow. Patients with COPD are at high risk for severe respiratory symptoms upon influenza virus infection. Airway epithelial cells provide the first-line antiviral defense, but whether or not their susceptibility and response to influenza virus infection changes in COPD have not been elucidated. Therefore, this study aimed to compare the susceptibility of COPD- and control-derived airway epithelium to the influenza virus and assess protein changes during influenza virus infection by quantitative proteomics. Materials and methods The presence of human- and avian-type influenza A virus receptor was assessed in control and COPD lung sections as well as in fully differentiated primary human bronchial epithelial cells (phBECs) by lectin- or antibody-based histochemical staining. PhBECs were from COPD lungs, including cells from moderate- and severe-stage diseases, and from age-, sex-, smoking, and history-matched control lung specimens. Protein profiles pre- and post-influenza virus infection in vitro were directly compared using quantitative proteomics, and selected findings were validated by qRT-PCR and immunoblotting. Results The human-type influenza receptor was more abundant in human airways than the avian-type influenza receptor, a property that was retained in vitro when differentiating phBECs at the air-liquid interface. Proteomics of phBECs pre- and post-influenza A virus infection with A/Puerto Rico/8/34 (PR8) revealed no significant differences between COPD and control phBECs in terms of flu receptor expression, cell type composition, virus replication, or protein profile pre- and post-infection. Independent of health state, a robust antiviral response to influenza virus infection was observed, as well as upregulation of several novel influenza virus-regulated proteins, including PLSCR1, HLA-F, CMTR1, DTX3L, and SHFL. Conclusion COPD- and control-derived phBECs did not differ in cell type composition, susceptibility to influenza virus infection, and proteomes pre- and post-infection. Finally, we identified novel influenza A virus-regulated proteins in bronchial epithelial cells that might serve as potential targets to modulate the pathogenicity of infection and acute exacerbations.
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Affiliation(s)
- Misako Nakayama
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M BioArchive, Helmholtz Zentrum München, Member of the German Center of Lung Research (DZL), Munich, Germany,Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
| | - Hannah Marchi
- Core Facility Statistical Consulting, Helmholtz Zentrum München, Munich, Germany,Faculty of Business Administration and Economics, Bielefeld University, Bielefeld, Germany
| | - Anna M. Dmitrieva
- Research Unit Lung Repair and Regeneration, Helmholtz Zentrum München, Member of the German Center of Lung Research (DZL), Munich, Germany
| | - Ashesh Chakraborty
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M BioArchive, Helmholtz Zentrum München, Member of the German Center of Lung Research (DZL), Munich, Germany
| | - Juliane Merl-Pham
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Neuherberg, Germany
| | - Elisabeth Hennen
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M BioArchive, Helmholtz Zentrum München, Member of the German Center of Lung Research (DZL), Munich, Germany
| | - Ronan Le Gleut
- Core Facility Statistical Consulting, Helmholtz Zentrum München, Munich, Germany
| | - Clemens Ruppert
- Department of Internal Medicine, Medizinische Klinik II, Member of the German Center of Lung Research (DZL), Giessen, Germany
| | - Andreas Guenther
- Department of Internal Medicine, Medizinische Klinik II, Member of the German Center of Lung Research (DZL), Giessen, Germany
| | - Kathrin Kahnert
- Department of Medicine V, Ludwig Maximilian University (LMU) Munich, Member of the German Center of Lung Research, University Hospital, Munich, Germany
| | - Jürgen Behr
- Department of Medicine V, Ludwig Maximilian University (LMU) Munich, Member of the German Center of Lung Research, University Hospital, Munich, Germany
| | - Anne Hilgendorff
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M BioArchive, Helmholtz Zentrum München, Member of the German Center of Lung Research (DZL), Munich, Germany
| | - Stefanie M. Hauck
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Neuherberg, Germany
| | - Heiko Adler
- Research Unit Lung Repair and Regeneration, Helmholtz Zentrum München, Member of the German Center of Lung Research (DZL), Munich, Germany,Institute of Asthma and Allergy Prevention, Helmholtz Zentrum München, Member of the German Center of Lung Research (DZL), Munich, Germany,*Correspondence: Heiko Adler,
| | - Claudia A. Staab-Weijnitz
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M BioArchive, Helmholtz Zentrum München, Member of the German Center of Lung Research (DZL), Munich, Germany,Claudia A. Staab-Weijnitz, ; https://orcid.org/0000-0002-1211-7834
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Zeng L, Chen K, Xiao F, Zhu CY, Bai JY, Tan S, Long L, Wang Y, Zhou Q. Potential common molecular mechanisms between Sjögren syndrome and inclusion body myositis: a bioinformatic analysis and in vivo validation. Front Immunol 2023; 14:1161476. [PMID: 37153570 PMCID: PMC10160489 DOI: 10.3389/fimmu.2023.1161476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/07/2023] [Indexed: 05/09/2023] Open
Abstract
Background Inclusion body myositis (IBM) is a slowly progressive inflammatory myopathy that typically affects the quadriceps and finger flexors. Sjögren's syndrome (SS), an autoimmune disorder characterized by lymphocytic infiltration of exocrine glands has been reported to share common genetic and autoimmune pathways with IBM. However, the exact mechanism underlying their commonality remains unclear. In this study, we investigated the common pathological mechanisms involved in both SS and IBM using a bioinformatic approach. Methods IBM and SS gene expression profiles were obtained from the Gene Expression Omnibus (GEO). SS and IBM coexpression modules were identified using weighted gene coexpression network analysis (WGCNA), and differentially expressed gene (DEG) analysis was applied to identify their shared DEGs. The hidden biological pathways were revealed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Furthermore, protein-protein interaction (PPI) networks, cluster analyses, and hub shared gene identification were conducted. The expression of hub genes was validated by reverse transcription quantitative polymerase chain reaction (RT-qPCR). We then analyzed immune cell abundance patterns in SS and IBM using single-sample gene set enrichment analysis (ssGSEA) and investigated their association with hub genes. Finally, NetworkAnalyst was used to construct a common transcription factor (TF)-gene network. Results Using WGCNA, we found that 172 intersecting genes were closely related to viral infection and antigen processing/presentation. Based on DEG analysis, 29 shared genes were found to be upregulated and enriched in similar biological pathways. By intersecting the top 20 potential hub genes from the WGCNA and DEG sets, three shared hub genes (PSMB9, CD74, and HLA-F) were derived and validated to be active transcripts, which all exhibited diagnostic values for SS and IBM. Furthermore, ssGSEA showed similar infiltration profiles in IBM and SS, and the hub genes were positively correlated with the abundance of immune cells. Ultimately, two TFs (HDGF and WRNIP1) were identified as possible key TFs. Conclusion Our study identified that IBM shares common immunologic and transcriptional pathways with SS, such as viral infection and antigen processing/presentation. Furthermore, both IBM and SS have almost identical immune infiltration microenvironments, indicating similar immune responses may contribute to their association.
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Affiliation(s)
- Li Zeng
- Department of Neurology, Sichuan Academy of Medical Science and Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Kai Chen
- Department of Neurology, Sichuan Academy of Medical Science and Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Feng Xiao
- Department of Neurology, Sichuan Academy of Medical Science and Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Chun-yan Zhu
- Department of Neurology, Sichuan Academy of Medical Science and Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Jia-ying Bai
- Department of Neurology, Sichuan Academy of Medical Science and Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Song Tan
- Department of Neurology, Sichuan Academy of Medical Science and Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, Chengdu, China
| | - Li Long
- Department of Rheumatology and Immunology, Sichuan Academy of Medical Science and Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- *Correspondence: Qiao Zhou, ; Yi Wang, ; Li Long,
| | - Yi Wang
- Department of Critical Care Medicine, Sichuan Academy of Medical Science and Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- *Correspondence: Qiao Zhou, ; Yi Wang, ; Li Long,
| | - Qiao Zhou
- Department of Rheumatology and Immunology, Sichuan Academy of Medical Science and Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Clinical Immunology Translational Medicine Key Laboratory of Sichuan Province, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- *Correspondence: Qiao Zhou, ; Yi Wang, ; Li Long,
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Arnaiz-Villena A, Suarez-Trujillo F, Juarez I, Rodríguez-Sainz C, Palacio-Gruber J, Vaquero-Yuste C, Molina-Alejandre M, Fernández-Cruz E, Martin-Villa JM. Evolution and molecular interactions of major histocompatibility complex (MHC)-G, -E and -F genes. Cell Mol Life Sci 2022; 79:464. [PMID: 35925520 PMCID: PMC9352621 DOI: 10.1007/s00018-022-04491-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 07/12/2022] [Accepted: 07/15/2022] [Indexed: 11/30/2022]
Abstract
Classical HLA (Human Leukocyte Antigen) is the Major Histocompatibility Complex (MHC) in man. HLA genes and disease association has been studied at least since 1967 and no firm pathogenic mechanisms have been established yet. HLA-G immune modulation gene (and also -E and -F) are starting the same arduous way: statistics and allele association are the trending subjects with the same few results obtained by HLA classical genes, i.e., no pathogenesis may be discovered after many years of a great amount of researchers’ effort. Thus, we believe that it is necessary to follow different research methodologies: (1) to approach this problem, based on how evolution has worked maintaining together a cluster of immune-related genes (the MHC) in a relatively short chromosome area since amniotes to human at least, i.e., immune regulatory genes (MHC-G, -E and -F), adaptive immune classical class I and II genes, non-adaptive immune genes like (C2, C4 and Bf) (2); in addition to using new in vitro models which explain pathogenetics of HLA and disease associations. In fact, this evolution may be quite reliably studied during about 40 million years by analyzing the evolution of MHC-G, -E, -F, and their receptors (KIR—killer-cell immunoglobulin-like receptor, NKG2—natural killer group 2-, or TCR-T-cell receptor—among others) in the primate evolutionary lineage, where orthology of these molecules is apparently established, although cladistic studies show that MHC-G and MHC-B genes are the ancestral class I genes, and that New World apes MHC-G is paralogous and not orthologous to all other apes and man MHC-G genes. In the present review, we outline past and possible future research topics: co-evolution of adaptive MHC classical (class I and II), non-adaptive (i.e., complement) and modulation (i.e., non-classical class I) immune genes may imply that the study of full or part of MHC haplotypes involving several loci/alleles instead of single alleles is important for uncovering HLA and disease pathogenesis. It would mainly apply to starting research on HLA-G extended haplotypes and disease association and not only using single HLA-G genetic markers.
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Affiliation(s)
- Antonio Arnaiz-Villena
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense de Madrid, Pabellón 5, planta 4. Avda. Complutense s/n, 28040, Madrid, Spain.
| | - Fabio Suarez-Trujillo
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense de Madrid, Pabellón 5, planta 4. Avda. Complutense s/n, 28040, Madrid, Spain
| | - Ignacio Juarez
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense de Madrid, Pabellón 5, planta 4. Avda. Complutense s/n, 28040, Madrid, Spain
| | - Carmen Rodríguez-Sainz
- Instituto de Investigaciones Sanitarias Gregorio Marañón, Hospital Gregorio Marañón, Madrid, Spain
| | - José Palacio-Gruber
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense de Madrid, Pabellón 5, planta 4. Avda. Complutense s/n, 28040, Madrid, Spain
| | - Christian Vaquero-Yuste
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense de Madrid, Pabellón 5, planta 4. Avda. Complutense s/n, 28040, Madrid, Spain
| | - Marta Molina-Alejandre
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense de Madrid, Pabellón 5, planta 4. Avda. Complutense s/n, 28040, Madrid, Spain
| | - Eduardo Fernández-Cruz
- Instituto de Investigaciones Sanitarias Gregorio Marañón, Hospital Gregorio Marañón, Madrid, Spain
| | - José Manuel Martin-Villa
- Departamento de Inmunología, Facultad de Medicina, Universidad Complutense de Madrid, Pabellón 5, planta 4. Avda. Complutense s/n, 28040, Madrid, Spain
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Scherm MG, Wyatt RC, Serr I, Anz D, Richardson SJ, Daniel C. Beta cell and immune cell interactions in autoimmune type 1 diabetes: How they meet and talk to each other. Mol Metab 2022; 64:101565. [PMID: 35944899 PMCID: PMC9418549 DOI: 10.1016/j.molmet.2022.101565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/08/2022] [Accepted: 07/27/2022] [Indexed: 10/31/2022] Open
Abstract
Background Scope of review Major conclusions
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Suzuki S, Morishima S, Murata M, Tanaka M, Shigenari A, Ito S, Kanga U, Kulski JK, Morishima Y, Shiina T. Sequence Variations Within HLA-G and HLA-F Genomic Segments at the Human Leukocyte Antigen Telomeric End Associated With Acute Graft-Versus-Host Disease in Unrelated Bone Marrow Transplantation. Front Immunol 2022; 13:938206. [PMID: 35935961 PMCID: PMC9351719 DOI: 10.3389/fimmu.2022.938206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Acute graft-versus-host disease (aGVHD) is defined as a syndrome of an immunological response of graft to the host that occurs early after allogeneic hematopoietic stem cell transplantation (HCT). This disease is frequently observed even in HCT matched for human leukocyte antigen (HLA) alleles at multiple gene loci. Although the HLA region represents complex and diverse genomic characteristics, detailed association analysis is required for the identification of uncharacterized variants that are strongly associated with aGVHD. We genotyped three loci, OR2H2, HLA-F-AS1, and HLA-G, that are located in the 460 kb of HLA telomeric region and statistically analyzed the genotypes including HLA-DPB1 with clinical and transplantation outcomes using 338 unrelated bone marrow transplantation (UR-BMT) patient–donor pairs who were matched for HLA-A, HLA-B, HLA-C, HLA-DRB1, and HLA-DQB1 (HLA-10/10). Multivariate analyses demonstrated that HLA-F-AS1 and HLA-DPB1 mismatches were associated with grade II–IV aGVHD (hazard ratio (HR), 1.76; 95% CI, 1.07–2.88; p = 0.026; and HR, 1.59; CI, 1.02–2.49; p = 0.042, respectively). There was no confounding between HLA-F-AS1 and HLA-DPB1 (p = 0.512), suggesting that the HLA-F-AS1 mismatch has a strong effect on aGVHD independently of HLA-DPB1. Moreover, a stratified analysis suggested possible associations of HLA-F-AS1, HLA-DPB1, and/or HLA-G mismatches with grade II–IV aGVHD and the more severe grade III–IV aGVHD. These findings provide new insights into understanding the molecular mechanism of aGVHD caused by HLA-matched UR-BMT.
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Affiliation(s)
- Shingo Suzuki
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Satoko Morishima
- Division of Endocrinology, Diabetes and Metabolism, Hematology, Rheumatology, Second Department of Internal Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Makoto Murata
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masafumi Tanaka
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Atsuko Shigenari
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Sayaka Ito
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Uma Kanga
- Clinical Immunogenetics Laboratory, Centre for Excellence in Molecular Medicine, Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Jerzy K. Kulski
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
- Faculty of Health and Medical Sciences, The University of Western Australia Medical School, Crawley, WA, Australia
| | - Yasuo Morishima
- Department of Promotion for Blood and Marrow Transplantation, Aichi Medical University School of Medicine, Nagakute, Japan
- Department of Hematology and Oncology, Nakagami Hospital, Okinawa, Japan
| | - Takashi Shiina
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
- *Correspondence: Takashi Shiina,
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20
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Raghubar AM, Pham DT, Tan X, Grice LF, Crawford J, Lam PY, Andersen SB, Yoon S, Teoh SM, Matigian NA, Stewart A, Francis L, Ng MSY, Healy HG, Combes AN, Kassianos AJ, Nguyen Q, Mallett AJ. Spatially Resolved Transcriptomes of Mammalian Kidneys Illustrate the Molecular Complexity and Interactions of Functional Nephron Segments. Front Med (Lausanne) 2022; 9:873923. [PMID: 35872784 PMCID: PMC9300864 DOI: 10.3389/fmed.2022.873923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 05/23/2022] [Indexed: 11/30/2022] Open
Abstract
Available transcriptomes of the mammalian kidney provide limited information on the spatial interplay between different functional nephron structures due to the required dissociation of tissue with traditional transcriptome-based methodologies. A deeper understanding of the complexity of functional nephron structures requires a non-dissociative transcriptomics approach, such as spatial transcriptomics sequencing (ST-seq). We hypothesize that the application of ST-seq in normal mammalian kidneys will give transcriptomic insights within and across species of physiology at the functional structure level and cellular communication at the cell level. Here, we applied ST-seq in six mice and four human kidneys that were histologically absent of any overt pathology. We defined the location of specific nephron structures in the captured ST-seq datasets using three lines of evidence: pathologist's annotation, marker gene expression, and integration with public single-cell and/or single-nucleus RNA-sequencing datasets. We compared the mouse and human cortical kidney regions. In the human ST-seq datasets, we further investigated the cellular communication within glomeruli and regions of proximal tubules–peritubular capillaries by screening for co-expression of ligand–receptor gene pairs. Gene expression signatures of distinct nephron structures and microvascular regions were spatially resolved within the mouse and human ST-seq datasets. We identified 7,370 differentially expressed genes (padj < 0.05) distinguishing species, suggesting changes in energy production and metabolism in mouse cortical regions relative to human kidneys. Hundreds of potential ligand–receptor interactions were identified within glomeruli and regions of proximal tubules–peritubular capillaries, including known and novel interactions relevant to kidney physiology. Our application of ST-seq to normal human and murine kidneys confirms current knowledge and localization of transcripts within the kidney. Furthermore, the generated ST-seq datasets provide a valuable resource for the kidney community that can be used to inform future research into this complex organ.
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Affiliation(s)
- Arti M. Raghubar
- Kidney Health Service, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
- Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Anatomical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Duy T. Pham
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Xiao Tan
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Laura F. Grice
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Joanna Crawford
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Pui Yeng Lam
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Stacey B. Andersen
- Genome Innovation Hub, University of Queensland, Brisbane, QLD, Australia
- UQ Sequencing Facility, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Sohye Yoon
- Genome Innovation Hub, University of Queensland, Brisbane, QLD, Australia
| | - Siok Min Teoh
- UQ Diamantina Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD, Australia
| | - Nicholas A. Matigian
- QCIF Facility for Advanced Bioinformatics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Anne Stewart
- Anatomical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia
| | - Leo Francis
- Anatomical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia
| | - Monica S. Y. Ng
- Kidney Health Service, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
- Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- Nephrology Department, Princess Alexandra Hospital, Woolloongabba, QLD, Australia
| | - Helen G. Healy
- Kidney Health Service, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
- Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Alexander N. Combes
- Department of Anatomy and Developmental Biology, Stem Cells and Development Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Andrew J. Kassianos
- Kidney Health Service, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
- Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Quan Nguyen
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- *Correspondence: Andrew J. Mallett
| | - Andrew J. Mallett
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- College of Medicine & Dentistry, James Cook University, Townsville, Queensland, QLD, Australia
- Department of Renal Medicine, Townsville University Hospital, Townsville, Queensland, QLD, Australia
- Quan Nguyen
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21
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Papúchová H, Saxtorph MH, Hallager T, Jepsen IE, Eriksen JO, Persson G, Funck T, Weisdorf I, Macklon NS, Larsen LG, Hviid TVF. Endometrial HLA-F expression is influenced by genotypes and correlates differently with immune cell infiltration in IVF and recurrent implantation failure patients. Hum Reprod 2022; 37:1816-1834. [PMID: 35689445 DOI: 10.1093/humrep/deac118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 05/01/2022] [Indexed: 12/11/2022] Open
Abstract
STUDY QUESTION Is human leukocyte antigen (HLA)-F protein expressed in mid-secretory endometrium, and are its expression levels influenced by HLA-F gene polymorphisms and correlated with the abundance of uterine natural killer (uNK) cells and anti-inflammatory M2 macrophages? SUMMARY ANSWER HLA-F protein is expressed in mid-secretory endometrium, and levels are correlated with immune cell infiltration, plasma progesterone concentrations and HLA-F single-nucleotide polymorphisms (SNPs), however, women experiencing recurrent implantation failure (RIF) show differences when compared to women attending their first IVF treatment. WHAT IS KNOWN ALREADY The immunomodulatory HLA class Ib molecules HLA-G and HLA-F are expressed on the extravillous trophoblast cells and interact with receptors on maternal immune cells. Little is known regarding HLA-F expression in endometrial stroma and HLA-F function; furthermore, HLA-F and HLA-G SNP genotypes and haplotypes have been correlated with differences in time-to-pregnancy. STUDY DESIGN, SIZE, DURATION Primary endometrial stromal cell (ESC) cultures (n = 5) were established from endometrial biopsies from women attending IVF treatment at a fertility clinic. Basic HLA-F and HLA-G protein expression by the ESCs were investigated. A prospective controlled cohort study was performed including 85 women with a history of RIF and 36 control women beginning their first fertility treatment and with no history of RIF. In some analyses, the RIF group was divided into unknown cause, male infertility, female infertility, and both female and male infertility. Endometrial biopsies and blood samples were obtained the day equivalent to embryo transfer in a hormone-substituted cycle. PARTICIPANTS/MATERIALS, SETTING, METHODS HLA protein expression by ESCs was characterized using flow cytometry and western blot. In the cohort study, the specific immune markers HLA-F and HLA-G, CD56 and CD16 (NK cells), CD163 (M2 macrophages), FOXP3 (regulatory T cells) and CD138 (plasma cells) were analysed by immunohistochemistry and a digital image analysis system in endometrial biopsies. Endometrial receptivity was assessed by an endometrial receptivity array test (the ERA® test). Endometrial biopsies were examined according to modified Noyes' criteria. SNPs at the HLA-F gene and HLA-G haplotypes were determined. MAIN RESULTS AND THE ROLE OF CHANCE HLA-F protein is expressed in the endometrium at the time of implantation. Furthermore, the HLA-F protein levels were different according to the womeńs HLA-F SNP genotypes and diplotypes, which have previously been correlated with differences in time-to-pregnancy. Endometrial HLA-F was positively correlated with anti-inflammatory CD163+ M2 macrophage infiltration and CD56+ uNK cell abundance for the entire cohort. However, this was not the case for CD56+ in the female infertility RIF subgroup. HLA-F levels in the endometrial stroma were negatively correlated with plasma progesterone concentrations in the RIF subgroup with known female infertility. Conversely, HLA-F and progesterone were positively correlated in the RIF subgroup with infertility of the male partner and no infertility diagnosis of the woman indicating interconnections between progesterone, HLA-F and immune cell infiltration. Glandular sHLA-G expression was also positively correlated with uNK cell abundance in the RIF subgroup with no female infertility but negatively correlated in the RIF subgroup with a female infertility diagnosis. LARGE SCALE DATA Immunohistochemistry analyses of endometrial biopsies and DNA sequencing of HLA genes. Data will be shared upon reasonable request to the corresponding author. LIMITATIONS, REASONS FOR CAUTION The control group of women attending their first IVF treatment had an anticipated good prognosis but was not proven fertile. A significant age difference between the RIF group and the IVF group reflects the longer treatment period for women with a history of RIF. The standardization of hormonal endometrial preparation, which allowed consistent timing of endometrial and blood sampling, might be a strength because a more uniform hormonal background may more clearly show an influence on the immune marker profile and HLA class Ib levels in the endometrium by other factors, for example genetic polymorphisms. However, the immune marker profile might be different during a normal cycle. WIDER IMPLICATIONS OF THE FINDINGS The findings further highlight the importance of HLA-F and HLA-G at the implantation site and in early pregnancy for pregnancy success. Diagnostic measures and modulation of the complex interactions between HLA class Ib molecules, maternal immune cells and hormonal factors may have potential to improve fertility treatment. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by the Region Zealand Health Sciences Research Foundation and the Zealand University Hospital through the ReproHealth Research Consortium ZUH. The authors declared there are no conflicts of interest.
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Affiliation(s)
- Henrieta Papúchová
- Department of Clinical Biochemistry, Centre for Immune Regulation and Reproductive Immunology (CIRRI), Zealand University Hospital, Roskilde, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.,The ReproHealth Research Consortium, Zealand University Hospital, Denmark
| | - Malene Hviid Saxtorph
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.,The ReproHealth Research Consortium, Zealand University Hospital, Denmark.,Department of Obstetrics and Gynaecology, The Fertility Clinic, Zealand University Hospital, Denmark
| | - Trine Hallager
- The ReproHealth Research Consortium, Zealand University Hospital, Denmark.,Department of Pathology, Zealand University Hospital, Roskilde, Denmark
| | - Ida E Jepsen
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.,The ReproHealth Research Consortium, Zealand University Hospital, Denmark.,Department of Obstetrics and Gynaecology, The Fertility Clinic, Zealand University Hospital, Denmark
| | - Jens O Eriksen
- The ReproHealth Research Consortium, Zealand University Hospital, Denmark.,Department of Pathology, Zealand University Hospital, Roskilde, Denmark
| | - Gry Persson
- Department of Clinical Biochemistry, Centre for Immune Regulation and Reproductive Immunology (CIRRI), Zealand University Hospital, Roskilde, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.,The ReproHealth Research Consortium, Zealand University Hospital, Denmark
| | - Tina Funck
- Department of Clinical Biochemistry, Centre for Immune Regulation and Reproductive Immunology (CIRRI), Zealand University Hospital, Roskilde, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.,The ReproHealth Research Consortium, Zealand University Hospital, Denmark
| | - Iben Weisdorf
- Department of Clinical Biochemistry, Centre for Immune Regulation and Reproductive Immunology (CIRRI), Zealand University Hospital, Roskilde, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.,The ReproHealth Research Consortium, Zealand University Hospital, Denmark
| | - Nicholas S Macklon
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.,The ReproHealth Research Consortium, Zealand University Hospital, Denmark.,Department of Obstetrics and Gynaecology, The Fertility Clinic, Zealand University Hospital, Denmark.,London Women's Clinic, London, UK
| | - Lise Grupe Larsen
- The ReproHealth Research Consortium, Zealand University Hospital, Denmark.,Department of Pathology, Zealand University Hospital, Roskilde, Denmark
| | - Thomas Vauvert F Hviid
- Department of Clinical Biochemistry, Centre for Immune Regulation and Reproductive Immunology (CIRRI), Zealand University Hospital, Roskilde, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.,The ReproHealth Research Consortium, Zealand University Hospital, Denmark
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22
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Wong NKY, Dong X, Lin YY, Xue H, Wu R, Lin D, Collins C, Wang Y. Framework of Intrinsic Immune Landscape of Dormant Prostate Cancer. Cells 2022; 11:cells11091550. [PMID: 35563856 PMCID: PMC9105276 DOI: 10.3390/cells11091550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 02/01/2023] Open
Abstract
Androgen deprivation therapy (ADT) is the standard therapy for men with advanced prostate cancer (PCa). PCa often responds to ADT and enters a dormancy period, which can be recognized clinically as a minimal residual disease. However, the majority of these patients will eventually experience a relapse in the form of castration-resistant PCa with poor survival. Therefore, ADT-induced dormancy is a unique time window for treatment that can provide a cure. The study of this well-recognized phase of prostate cancer progression is largely hindered by the scarcity of appropriate clinical tissue and clinically relevant preclinical models. Here, we report the utility of unique and clinically relevant patient-derived xenograft models in the study of the intrinsic immune landscape of dormant PCa. Using data from RNA sequencing, we have reconstructed the immune evasion mechanisms that can be utilized by dormant PCa cells. Since dormant PCa cells need to evade the host immune surveillance for survival, our results provide a framework for further study and for devising immunomodulatory mechanisms that can eliminate dormant PCa cells.
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Affiliation(s)
- Nelson K. Y. Wong
- Department of Experimental Therapeutics, BC Cancer, 675 W 10th Ave, Vancouver, BC V5Z 1L3 Canada; (N.K.Y.W.); (X.D.); (H.X.); (R.W.); (D.L.)
| | - Xin Dong
- Department of Experimental Therapeutics, BC Cancer, 675 W 10th Ave, Vancouver, BC V5Z 1L3 Canada; (N.K.Y.W.); (X.D.); (H.X.); (R.W.); (D.L.)
| | - Yen-Yi Lin
- Vancouver Prostate Centre, Department of Urologic Sciences, Faculty of Medicine, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada; (Y.-Y.L.); (C.C.)
| | - Hui Xue
- Department of Experimental Therapeutics, BC Cancer, 675 W 10th Ave, Vancouver, BC V5Z 1L3 Canada; (N.K.Y.W.); (X.D.); (H.X.); (R.W.); (D.L.)
| | - Rebecca Wu
- Department of Experimental Therapeutics, BC Cancer, 675 W 10th Ave, Vancouver, BC V5Z 1L3 Canada; (N.K.Y.W.); (X.D.); (H.X.); (R.W.); (D.L.)
| | - Dong Lin
- Department of Experimental Therapeutics, BC Cancer, 675 W 10th Ave, Vancouver, BC V5Z 1L3 Canada; (N.K.Y.W.); (X.D.); (H.X.); (R.W.); (D.L.)
| | - Colin Collins
- Vancouver Prostate Centre, Department of Urologic Sciences, Faculty of Medicine, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada; (Y.-Y.L.); (C.C.)
| | - Yuzhuo Wang
- Department of Experimental Therapeutics, BC Cancer, 675 W 10th Ave, Vancouver, BC V5Z 1L3 Canada; (N.K.Y.W.); (X.D.); (H.X.); (R.W.); (D.L.)
- Vancouver Prostate Centre, Department of Urologic Sciences, Faculty of Medicine, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada; (Y.-Y.L.); (C.C.)
- Correspondence: ; Tel.: +1-604-675-8013
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23
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Lyu M, Zhou J, Jiao L, Wang Y, Zhou Y, Lai H, Xu W, Ying B. Deciphering a TB-related DNA methylation biomarker and constructing a TB diagnostic classifier. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:37-49. [PMID: 34938605 PMCID: PMC8645423 DOI: 10.1016/j.omtn.2021.11.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 11/16/2021] [Indexed: 02/09/2023]
Abstract
We systemically identified tuberculosis (TB)-related DNA methylation biomarkers and further constructed classifiers for TB diagnosis. TB-related DNA methylation datasets were searched through October 3, 2020. Limma and DMRcate were employed to identify differentially methylated probes (DMPs) and regions (DMRs). Machine learning methods were used to construct classifiers. The performance of the classifiers was evaluated in discovery datasets and a prospective independent cohort. Eighty-nine DMPs and 24 DMRs were identified based on 67 TB patients and 45 healthy controls from 4 datasets. Nine and three DMRs were selected by elastic net regression and logistic regression, respectively. Among the selected DMRs, two regions (chr3: 195635643-195636243 and chr6: 29691631-29692475) were differentially methylated in the independent cohort (p = 4.19 × 10-5 and 0.024, respectively). Among the ten classifiers, the 3-DMR logistic regression classifier exhibited the strongest performance. The sensitivity, specificity, and area under the curve were, respectively, 79.1%, 84.4%, and 0.888 in the discovery datasets and 64.5%, 90.3%, and 0.838 in the independent cohort. The differential diagnostic ability of this classifier was also assessed. Collectively, these data showed that DNA methylation might be a promising TB diagnostic biomarker. The 3-DMR logistic regression classifier is a potential clinical tool for TB diagnosis, and further validation is needed.
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Affiliation(s)
- Mengyuan Lyu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, No. 37, Guoxue Alley, Chengdu, Sichuan 610041, China.,West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jian Zhou
- West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China.,Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Lin Jiao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, No. 37, Guoxue Alley, Chengdu, Sichuan 610041, China.,West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yili Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, No. 37, Guoxue Alley, Chengdu, Sichuan 610041, China.,West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yanbing Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, No. 37, Guoxue Alley, Chengdu, Sichuan 610041, China.,West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Hongli Lai
- West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, 10-511, 610 University Avenue, Toronto, ON M5G 2M9 Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7 Canada
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, No. 37, Guoxue Alley, Chengdu, Sichuan 610041, China.,West China School of Medicine, Sichuan University, Chengdu, Sichuan 610041, China
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24
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Ramifications of the HLA-I Allelic Reactivity of Anti-HLA-E*01:01 and Anti-HLA-E*01:03 Heavy Chain Monoclonal Antibodies in Comparison with Anti-HLA-I IgG Reactivity in Non-Alloimmunized Males, Melanoma-Vaccine Recipients, and End-Stage Renal Disease Patients. Antibodies (Basel) 2022; 11:antib11010018. [PMID: 35323192 PMCID: PMC8944535 DOI: 10.3390/antib11010018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/07/2022] [Accepted: 02/22/2022] [Indexed: 01/19/2023] Open
Abstract
Serum anti-HLA-I IgG are present in non-alloimmunized males, cancer patients, and transplant recipients. Anti-HLA-I antibodies are also present in intravenous immunoglobulin (IVIg), prepared from the plasma of thousands of healthy donors. However, the HLA-Ia reactivity of IVIg diminishes markedly after passing through HLA-E HC-affinity columns, suggesting that the HLA-I reactivity is due to antibodies formed against HLA-E. Hence, we examined whether anti-HLA-E antibodies can react to HLA-I alleles. Monoclonal IgG antibodies (mAbs) against HCs of two HLA-E alleles were generated in Balb/C mice. The antibodies were analyzed using multiplex bead assays on a Luminex platform for HLA-I reactivity. Beads coated with an array of HLA heterodimers admixed with HCs (LABScreen) were used to examine the binding of IgG to different HLA-Ia (31-HLA-A, 50-HLA-B, and 16-HLA-C) and Ib (2-HLA-E, one each of HLA-F and HLA-G) alleles. A striking diversity in the HLA-Ia and/or HLA-Ib reactivity of mAbs was observed. The number of the mAbs reactive to (1) only HLA-E (n = 25); (2) all HLA-Ib isomers (n = 8); (3) HLA-E and HLA-B (n = 5); (4) HLA-E, HLA-B, and HLA-C (n = 30); (5) HLA-E, HLA-A*1101, HLA-B, and HLA-C (n = 83); (6) HLA-E, HLA-A, HLA-B, and HLA-C (n = 54); and (7) HLA-Ib and HLA-Ia (n = 8), in addition to four other minor groups. Monospecificity and polyreactivity were corroborated by HLA-E monospecific and HLA-I shared sequences. The diverse HLA-I reactivity of the mAbs are compared with the pattern of HLA-I reactivity of serum-IgG in non-alloimmunized males, cancer patients, and ESKD patients. The findings unravel the diagnostic potential of the HLA-E monospecific-mAbs and immunomodulatory potentials of IVIg highly mimicking HLA-I polyreactive-mAbs.
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25
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Ravindranath MH, Ravindranath NM, Selvan SR, Filippone EJ, Amato-Menker CJ, El Hilali F. Four Faces of Cell-Surface HLA Class-I: Their Antigenic and Immunogenic Divergence Generating Novel Targets for Vaccines. Vaccines (Basel) 2022; 10:vaccines10020339. [PMID: 35214796 PMCID: PMC8878457 DOI: 10.3390/vaccines10020339] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/07/2022] [Accepted: 02/17/2022] [Indexed: 12/19/2022] Open
Abstract
Leukocyte cell-surface HLA-I molecules, involved in antigen presentation of peptides to CD8+ T-cells, consist of a heavy chain (HC) non-covalently linked to β2-microglobulin (β2m) (Face-1). The HC amino acid composition varies across all six isoforms of HLA-I, while that of β2m remains the same. Each HLA-allele differs in one or more amino acid sequences on the HC α1 and α2 helices, while several sequences among the three helices are conserved. HCs without β2m (Face-2) are also observed on human cells activated by malignancy, viral transformation, and cytokine or chemokine-mediated inflammation. In the absence of β2m, the monomeric Face-2 exposes immunogenic cryptic sequences on these cells as confirmed by HLA-I monoclonal antibodies (LA45, L31, TFL-006, and TFL-007). Furthermore, such exposure enables dimerization between two Face-2 molecules by SH-linkage, salt linkage, H-bonding, and van der Waal forces. In HLA-B27, the linkage between two heavy chains with cysteines at position of 67 of the amino acid residues was documented. Similarly, several alleles of HLA-A, B, C, E, F and G express cysteine at 67, 101, and 164, and additionally, HLA-G expresses cysteine at position 42. Thus, the monomeric HC (Face-2) can dimerize with another HC of its own allele, as homodimers (Face-3), or with a different HC-allele, as heterodimers (Face-4). The presence of Face-4 is well documented in HLA-F. The post-translational HLA-variants devoid of β2m may expose several cryptic linear and non-linear conformationally altered sequences to generate novel epitopes. The objective of this review, while unequivocally confirming the post-translational variants of HLA-I, is to highlight the scientific and clinical importance of the four faces of HLA and to prompt further research to elucidate their functions and their interaction with non-HLA molecules during inflammation, infection, malignancy and transplantation. Indeed, these HLA faces may constitute novel targets for passive and active specific immunotherapy and vaccines.
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Affiliation(s)
- Mepur H. Ravindranath
- Department of Hematology and Oncology, Children’s Hospital, Los Angeles, CA 90027, USA
- Emeritus Research Scientist at Terasaki Foundation Laboratory, Santa Monica, CA 90064, USA
- Correspondence:
| | - Narendranath M. Ravindranath
- Norris Dental Science Center, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90089, USA;
| | | | - Edward J. Filippone
- Division of Nephrology, Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19145, USA;
| | - Carly J. Amato-Menker
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, WV 26506, USA;
| | - Fatiha El Hilali
- The Faculty of Medicine and Pharmacy of Laayoune, Ibn Zohr University, Agadir 70000, Morocco;
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26
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The HLA-G Immune Checkpoint Plays a Pivotal Role in the Regulation of Immune Response in Autoimmune Diseases. Int J Mol Sci 2021; 22:ijms222413348. [PMID: 34948145 PMCID: PMC8706866 DOI: 10.3390/ijms222413348] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 12/11/2022] Open
Abstract
The human G-leukocyte antigen (HLA-G) molecule is a non-classical major histocompatibility complex (MHC) class I molecule. The pertinence of HLA-G has been investigated in numerous studies which have sought to elucidate the relevance of HLA-G in pathologic conditions, such as autoimmune diseases, cancers, and hematologic malignancies. One of the main goals of the current research on HLA-G is to use this molecule in clinical practice, either in diagnostics or as a therapeutic target. Since HLA-G antigens are currently considered as immunomodulatory molecules that are involved in reducing inflammatory and immune responses, in this review, we decided to focus on this group of antigens as potential determinants of progression in autoimmune diseases. This article highlights what we consider as recent pivotal findings on the immunomodulatory function of HLA-G, not only to establish the role of HLA-G in the human body, but also to explain how these proteins mediate the immune response.
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27
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Schwartz JC, Maccari G, Heimeier D, Hammond JA. Highly-contiguous bovine genomes underpin accurate functional analyses and updated nomenclature of MHC class I. HLA 2021; 99:167-182. [PMID: 34802191 DOI: 10.1111/tan.14494] [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: 09/16/2021] [Revised: 11/05/2021] [Accepted: 11/17/2021] [Indexed: 11/29/2022]
Abstract
The major histocompatibility complex (MHC) class I region of cattle is both highly polymorphic and, unlike many species, highly variable in gene content between haplotypes. Cattle MHC class I alleles were historically grouped by sequence similarity in the more conserved 3' end of the coding sequence to form phylogenetic allele groups. This has formed the basis of current cattle MHC class I nomenclature. We presently describe and compare five fully assembled MHC class I haplotypes using the latest cattle and yak genome assemblies. Of the five previously described "pseudogenes" in the cattle MHC class I region, Pseudogene 3 is putatively functional in all haplotypes and Pseudogene 6 and Pseudogene 7 are putatively functional in some haplotypes. This was reinforced by evidence of transcription. Based on full gene sequences as well as 3' coding sequence, we identified distinct subgroups of BoLA-3 and BoLA-6 that represent distinct genetic loci. We further examined allele-specific expression using transcriptomic data revealing that certain alleles are consistently weakly expressed compared to others. These observations will help to inform further studies into how MHC class I region variability influences T cell and natural killer cell functions in cattle.
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Affiliation(s)
| | - Giuseppe Maccari
- The Pirbright Institute, Pirbright, UK.,Anthony Nolan Research Institute, London, UK
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28
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Ma S, Ba Y, Ji H, Wang F, Du J, Hu S. Recognition of Tumor-Associated Antigens and Immune Subtypes in Glioma for mRNA Vaccine Development. Front Immunol 2021; 12:738435. [PMID: 34603319 PMCID: PMC8484904 DOI: 10.3389/fimmu.2021.738435] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/02/2021] [Indexed: 12/30/2022] Open
Abstract
Background Although mRNA vaccines have been efficient for combating a variety of tumors, their effectiveness against glioma remains unclear. There is growing evidence that immunophenotyping can reflect the comprehensive immune status and microenvironment of the tumor, which correlates closely with treatment response and vaccination potency. The purpose of this research was to screen for effective antigens in glioma that could be used for developing mRNA vaccines and to further differentiate the immune subtypes of glioma to create an selection criteria for suitable patients for vaccination. Methods Gene expression profiles and clinical data of 698 glioma samples were extracted from The Cancer Genome Atlas, and RNA_seq data of 1018 glioma samples was gathered from Chinese Glioma Genome Atlas. Gene Expression Profiling Interactive Analysis was used to determine differential expression genes and prognostic markers, cBioPortal software was used to verify gene alterations, and Tumor Immune Estimation Resource was used to investigate the relationships among genes and immune infiltrating cells. Consistency clustering was applied for consistent matrix construction and data aggregation, Gene oncology enrichment was performed for functional annotation, and a graph learning-based dimensionality reduction method was applied to describe the subtypes of immunity. Results Four overexpressed and mutated tumor antigens associated with poor prognosis and infiltration of antigen presenting cells were identified in glioma, including TP53, IDH1, C3, and TCF12. Besides, four immune subtypes of glioma (IS1-IS4) and 10 immune gene modules were identified consistently in the TCGA data. The immune subtypes had diverse molecular, cellular, and clinical features. IS1 and IS4 displayed an immune-activating phenotype and were associated with worse survival than the other two subtypes, while IS2 and IS3 had lower levels of tumor immune infiltration. Immunogenic cell death regulators and immune checkpoints were also diversely expressed in the four immune subtypes. Conclusion TP53, IDH1, C3, and TCF12 are effective antigens for the development of anti-glioma mRNA vaccines. We found four stable and repeatable immune subtypes of human glioma, the classification of the immune subtypes of glioma may play a crucial role in the predicting mRNA vaccine outcome.
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Affiliation(s)
- Shuai Ma
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Yixu Ba
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Hang Ji
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Fang Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jianyang Du
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Shaoshan Hu
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Department of Neurosurgery, Emergency Medicine Center, Zhejiang Provincial People's Hospital Affiliated to Hangzhou Medical College, Hangzhou, China
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29
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Li M, Chen J, Liu S, Sun X, Xu H, Gao Q, Chen X, Xi C, Huang D, Deng Y, Zhang F, Gao S, Qiu S, Tao X, Zhai J, Wei H, Yao H, Chen W. Spermine-Related DNA Hypermethylation and Elevated Expression of Genes for Collagen Formation are Susceptible Factors for Chemotherapy-Induced Hand-Foot Syndrome in Chinese Colorectal Cancer Patients. Front Pharmacol 2021; 12:746910. [PMID: 34539419 PMCID: PMC8440935 DOI: 10.3389/fphar.2021.746910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 08/13/2021] [Indexed: 01/06/2023] Open
Abstract
Hand-foot syndrome (HFS) is a common capecitabine-based chemotherapy-related adverse event (CRAE) in patients with colorectal cancer (CRC). It is of great significance to comprehensively identify susceptible factors for HFS, and further to elucidate the biomolecular mechanism of HFS susceptibility. We performed an untargeted multi-omics analysis integrating DNA methylation, transcriptome, and metabolome data of 63 Chinese CRC patients who had complete CRAE records during capecitabine-based chemotherapy. We found that the metabolome changes for each of matched plasma, urine, and normal colorectal tissue (CRT) in relation to HFS were characterized by chronic tissue damage, which was indicated by reduced nucleotide salvage, elevated spermine level, and increased production of endogenous cytotoxic metabolites. HFS-related transcriptome changes of CRT showed an overall suppressed inflammation profile but increased M2 macrophage polarization. HFS-related DNA methylation of CRT presented gene-specific hypermethylation on genes mainly for collagen formation. The hypermethylation was accumulated in the opensea and shore regions, which elicited a positive effect on gene expression. Additionally, we developed and validated models combining relevant biomarkers showing reasonably good discrimination performance with the area under the receiver operating characteristic curve values from 0.833 to 0.955. Our results demonstrated that the multi-omics variations associated with a profibrotic phenotype were closely related to HFS susceptibility. HFS-related biomolecular variations in CRT contributed more to the relevant biomolecular mechanism of HFS than in plasma and urine. Spermine-related DNA hypermethylation and elevated expression of genes for collagen formation were closely associated with HFS susceptibility. These findings provided new insights into the susceptible factors for chemotherapy-induced HFS, which can promote the implementation of individualized treatment against HFS.
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Affiliation(s)
- Mingming Li
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Jiani Chen
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Shaoqun Liu
- Department of Gastric Intestinal Surgery, Minhang Hospital, Fudan University, Shanghai, China
| | - Xiaomeng Sun
- Research Institute, GloriousMed Clinical Laboratory Co., Ltd., Shanghai, China
| | - Huilin Xu
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Qianmin Gao
- Department of General Surgery, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Xintao Chen
- Department of General Surgery, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Chaowen Xi
- Research Institute, GloriousMed Clinical Laboratory Co., Ltd., Shanghai, China
| | - Doudou Huang
- Traditional Chinese Medicine Resource and Technology Center, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yi Deng
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Feng Zhang
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Shouhong Gao
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Shi Qiu
- Traditional Chinese Medicine Resource and Technology Center, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xia Tao
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Jingwen Zhai
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Hua Wei
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai, China.,Department of Pharmacy, 905th Hospital of PLA Navy, Naval Medical University, Shanghai, China
| | - Houshan Yao
- Department of General Surgery, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Wansheng Chen
- Department of Pharmacy, Second Affiliated Hospital of Naval Medical University, Shanghai, China.,Traditional Chinese Medicine Resource and Technology Center, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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30
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Hazini A, Fisher K, Seymour L. Deregulation of HLA-I in cancer and its central importance for immunotherapy. J Immunother Cancer 2021; 9:e002899. [PMID: 34353849 PMCID: PMC8344275 DOI: 10.1136/jitc-2021-002899] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2021] [Indexed: 12/28/2022] Open
Abstract
It is now well accepted that many tumors undergo a process of clonal selection which means that tumor antigens arising at various stages of tumor progression are likely to be represented in just a subset of tumor cells. This process is thought to be driven by constant immunosurveillance which applies selective pressure by eliminating tumor cells expressing antigens that are recognized by T cells. It is becoming increasingly clear that the same selective pressure may also select for tumor cells that evade immune detection by acquiring deficiencies in their human leucocyte antigen (HLA) presentation pathways, allowing important tumor antigens to persist within cells undetected by the immune system. Deficiencies in antigen presentation pathway can arise by a variety of mechanisms, including genetic and epigenetic changes, and functional antigen presentation is a hard phenomenon to assess using our standard analytical techniques. Nevertheless, it is likely to have profound clinical significance and could well define whether an individual patient will respond to a particular type of therapy or not. In this review we consider the mechanisms by which HLA function may be lost in clinical disease, we assess the implications for current immunotherapy approaches using checkpoint inhibitors and examine the prognostic impact of HLA loss demonstrated in clinical trials so far. Finally, we propose strategies that might be explored for possible patient stratification.
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Affiliation(s)
- Ahmet Hazini
- Department of Oncology, University of Oxford, Oxford, Oxfordshire, UK
| | - Kerry Fisher
- Department of Oncology, University of Oxford, Oxford, Oxfordshire, UK
| | - Len Seymour
- Department of Oncology, University of Oxford, Oxford, Oxfordshire, UK
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31
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Sonon P, Collares CVA, Ferreira MLB, Almeida RS, Sadissou I, Cordeiro MT, de Fátima Militão de Albuquerque M, Castelli EC, Lucena-Silva N, Donadi EA. Peripheral spectrum neurological disorder after arbovirus infection is associated with HLA-F variants among Northeastern Brazilians. INFECTION GENETICS AND EVOLUTION 2021; 92:104855. [PMID: 33839310 DOI: 10.1016/j.meegid.2021.104855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 04/02/2021] [Accepted: 04/06/2021] [Indexed: 01/02/2023]
Abstract
INTRODUCTION Non-classical class I human leukocyte antigens (HLA) molecules are known to modulate the function of cytotoxic cells (NK and T CD8+) during viral infection by interacting with inhibitory/activating receptors. However, little is known about the HLA-E/-F genetic variability on arbovirus infections. METHODS We evaluated by massive parallel sequencing the full HLA-E/-F genetic diversity among patients infected during the arbovirus (ZIKV, DENV, and CHIKV) outbreak leading to a broad range of neurological complications in the Brazilian State of Pernambuco. In parallel, healthy blood donors from the same area were also studied. Plink and R software were used for genetic association study. To limit the false-positive results and enhance the reliability of the results, we adopted P-values <0.01 as significant levels. RESULTS Compared to controls, the HLA-F alleles: -1610 C (rs17875375), +1383 G (rs17178385), and +3537 A (rs17875384), all in complete linkage disequilibrium with each other (r2 = 1), were overrepresented in patients presenting peripheral spectrum disorders (PSD). The HLA-F*Distal-D haplotype that harbored the -1610 C allele exhibited a trend increase in PSD group. No associations were found for HLA-E. CONCLUSIONS Our findings showed that the HLA-F genetic background seems to be more important than HLA-E on the susceptibility to PSD complications.
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Affiliation(s)
- Paulin Sonon
- Immunogenetic Laboratory, Immunology Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Av. Moraes rego, s/n, Campus da UFPE, Cidade Universitária, 50670420 Recife, PE, Brazil; Ribeirão Preto Medical School, University of São Paulo, AV Bandeirantes, 3900, HC, Vila Monte Alegre, 14049900 Ribeirão Preto, SP, Brazil
| | - Cristhianna V A Collares
- Ribeirão Preto Medical School, University of São Paulo, AV Bandeirantes, 3900, HC, Vila Monte Alegre, 14049900 Ribeirão Preto, SP, Brazil
| | - Maria Lúcia Brito Ferreira
- Hospital da Restauração Gov. Paulo Guerra, Av. Gov. Agamenon Magalhães, s/n, Derby, 52171011 Recife, PE, Brazil
| | - Renata Santos Almeida
- Immunogenetic Laboratory, Immunology Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Av. Moraes rego, s/n, Campus da UFPE, Cidade Universitária, 50670420 Recife, PE, Brazil
| | - Ibrahim Sadissou
- Ribeirão Preto Medical School, University of São Paulo, AV Bandeirantes, 3900, HC, Vila Monte Alegre, 14049900 Ribeirão Preto, SP, Brazil
| | - Marli Tenório Cordeiro
- Virology Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Av. Moraes rego, s/n, Campus da UFPE, Cidade Universitária, 50670420 Recife, PE, Brazil
| | - Maria de Fátima Militão de Albuquerque
- Public Health Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Av. Moraes rego, s/n, Campus da UFPE, Cidade Universitária, 50670420 Recife, PE, Brazil
| | - Erick C Castelli
- São Paulo State University (UNESP), School of Medicine, Molecular Genetics and Bioinformatics Laboratory, Prof. Dr. Walter Maurício Correa, s/n Unesp, Campus de Botucatu, Botucatu CEP 18618681, SP, Brazil; São Paulo State University (UNESP), Department of Pathology, School of Medicine, Botucatu, SP, Brazil
| | - Norma Lucena-Silva
- Immunogenetic Laboratory, Immunology Department, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Av. Moraes rego, s/n, Campus da UFPE, Cidade Universitária, 50670420 Recife, PE, Brazil
| | - Eduardo A Donadi
- Ribeirão Preto Medical School, University of São Paulo, AV Bandeirantes, 3900, HC, Vila Monte Alegre, 14049900 Ribeirão Preto, SP, Brazil.
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32
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Persson G, Picard C, Marin G, Isgaard C, Stæhr CS, Molinari N, Chiaroni J, Lebech M, Hviid TVF, Di Cristofaro J. Maternal HLA Ib Polymorphisms in Pregnancy Allo-Immunization. Front Immunol 2021; 12:657217. [PMID: 33859649 PMCID: PMC8042285 DOI: 10.3389/fimmu.2021.657217] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/15/2021] [Indexed: 11/16/2022] Open
Abstract
During pregnancy the formation of alloreactive anti-human leukocyte antigen (HLA) antibodies are a major cause of acute rejection in organ transplantation and of adverse effects in blood transfusion. The purpose of the study was to identify maternal HLA class Ib genetic factors associated with anti-HLA allo-immunization in pregnancy and the degree of tolerance estimated by IgG4 expression. In total, 86 primiparous women with singleton pregnancies were included in the study. Maternal blood samples and umbilical cord samples were collected at delivery. Clinical data were obtained. Maternal blood serum was screened for HLA class I and II antibodies, identification of Donor Specific Antibody (DSA), activation of complement measured by C1q and IgG4 concentrations. Mothers were genotyped for HLA class Ib (HLA-E, -F and -G). Anti-HLA class I and II antibodies were identified in 24% of the women. The maternal HLA-E*01:06 allele was significantly associated with a higher fraction of anti-HLA I immunization (20.0% vs. 4.8%, p = 0.048). The maternal HLA-G 3’-untranslated region UTR4-HLA-G*01:01:01:05 haplotype and the HLA-F*01:03:01 allele were significantly associated with a low anti-HLA I C1q activation (16.7% vs. 57.1%, p = 0.028; 16.7% vs. 50.0%, p = 0.046; respectively). Both HLA‑G and HLA-F*01:03:01 showed significantly higher levels of IgG4 compared with the other haplotypes. The results support an association of certain HLA class Ib alleles with allo-immunization during pregnancy. Further studies are needed to elucidate the roles of HLA-E*01:06, HLA-F*01:03 and HLA‑G UTR4 in reducing the risk for allo-immunization.
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Affiliation(s)
- Gry Persson
- Centre for Immune Regulation and Reproductive Immunology (CIRRI), Department of Clinical Biochemistry, The ReproHealth Research Consortium ZUH, Zealand University Hospital, Roskilde, Denmark
| | - Christophe Picard
- Aix Marseille Univ, CNRS, EFS, ADES, "Biologie des Groupes Sanguins", Marseille, France.,Immunogenetics Laboratory, Etablissement français du Sang PACA Corse, Marseille, France
| | - Gregory Marin
- Unité de Recherche Clinique, Biostatistique et Epidémiologie, Département de l'Information Médicale (DIM) Hôpital La Colombière, Montpellier, France
| | - Cecilie Isgaard
- Centre for Immune Regulation and Reproductive Immunology (CIRRI), Department of Clinical Biochemistry, The ReproHealth Research Consortium ZUH, Zealand University Hospital, Roskilde, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Christina Seefeldt Stæhr
- Centre for Immune Regulation and Reproductive Immunology (CIRRI), Department of Clinical Biochemistry, The ReproHealth Research Consortium ZUH, Zealand University Hospital, Roskilde, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Nicolas Molinari
- Unité de Recherche Clinique, Biostatistique et Epidémiologie, Département de l'Information Médicale (DIM) Hôpital La Colombière, Montpellier, France
| | - Jacques Chiaroni
- Aix Marseille Univ, CNRS, EFS, ADES, "Biologie des Groupes Sanguins", Marseille, France
| | - Morten Lebech
- Department of Obstetrics and Gynecology, Zealand University Hospital, Roskilde, Denmark
| | - Thomas Vauvert F Hviid
- Centre for Immune Regulation and Reproductive Immunology (CIRRI), Department of Clinical Biochemistry, The ReproHealth Research Consortium ZUH, Zealand University Hospital, Roskilde, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Julie Di Cristofaro
- Aix Marseille Univ, CNRS, EFS, ADES, "Biologie des Groupes Sanguins", Marseille, France
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Chen X, Sun N, Li R, Sang X, Li X, Zhao J, Han J, Yang J, Ikezoe T. Targeting HLA-F suppresses the proliferation of glioma cells via a reduction in hexokinase 2-dependent glycolysis. Int J Biol Sci 2021; 17:1263-1276. [PMID: 33867844 PMCID: PMC8040476 DOI: 10.7150/ijbs.56357] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/15/2021] [Indexed: 12/19/2022] Open
Abstract
HLA-F, a nonclassical HLA class I molecule, is required for regulating immune tolerance. In recent years, HLA-F has been found to play a role in a variety of cancers, including glioma (GM). Additionally, high expression of HLA-F predicts the poor overall survival of individuals with GM. However, the functions of HLA-F in GM remain to be further elucidated. In this study, we found that HLA-F expression was elevated in GM tissues. High levels of HLA-F resulted in a high cell proliferation index and predicted GM recurrence. Forced expression of HLA-F promoted the growth of murine C8-D1A cells transplanted in immunodeficient Rag2-/- mice. In contrast, silencing HLA-F inhibited cell growth in vitro. Furthermore, targeting HLA-F with an anti-HLA-F antibody suppressed the growth of C8-D1A cells stably expressing HLA-F transplanted in immunodeficient Rag2-/- mice. In further experiments, we found that forced expression of HLA-F contributed to the aerobic glycolysis phenotype in C8-D1A cells along with an increase in HK2 protein stabilization. Conversely, silencing HK2 by shRNA reduced HLA-F-mediated glycolysis and cell proliferation. Our data indicated that HLA-F promoted cell proliferation via HK2-dependent glycolysis. HLA-F could be a potential therapeutic target for the treatment of GM.
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Affiliation(s)
- Xin Chen
- Jiangsu Province Key Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, China.,Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, China
| | - Na Sun
- Jiangsu Province Key Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, China.,Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, China
| | - Rongqin Li
- Jiangsu Province Key Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, China.,Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, China
| | - Xuejia Sang
- China University of Mining and Technology, Xuzhou, China
| | - Xueqin Li
- Jiangsu Province Key Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, China.,Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, China
| | - Jie Zhao
- Jiangsu Province Key Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, China.,Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, China
| | - Jing Han
- Jiangsu Province Key Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, China.,Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, China
| | - Jing Yang
- Jiangsu Province Key Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, China.,Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, China
| | - Takayuki Ikezoe
- The Department of Hematology, Fukushima Medical University, Fukushima, Japan
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Yelmen B, Marnetto D, Molinaro L, Flores R, Mondal M, Pagani L. Improving Selection Detection with Population Branch Statistic on Admixed Populations. Genome Biol Evol 2021; 13:6151747. [PMID: 33638983 PMCID: PMC8046333 DOI: 10.1093/gbe/evab039] [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] [Accepted: 02/22/2021] [Indexed: 12/16/2022] Open
Abstract
Detecting natural selection signals in admixed populations can be problematic since the source of the signal typically dates back prior to the admixture event. On one hand, it is now possible to study various source populations before a particular admixture thanks to the developments in ancient DNA (aDNA) in the last decade. However, aDNA availability is limited to certain geographical regions and the sample sizes and quality of the data might not be sufficient for selection analysis in many cases. In this study, we explore possible ways to improve detection of pre-admixture signals in admixed populations using a local ancestry inference approach. We used masked haplotypes for population branch statistic (PBS) and full haplotypes constructed following our approach from Yelmen et al. (2019) for cross-population extended haplotype homozygosity (XP-EHH), utilizing forward simulations to test the power of our analysis. The PBS results on simulated data showed that using masked haplotypes obtained from ancestry deconvolution instead of the admixed population might improve detection quality. On the other hand, XP-EHH results using the admixed population were better compared with the local ancestry method. We additionally report correlation for XP-EHH scores between source and admixed populations, suggesting that haplotype-based approaches must be used cautiously for recently admixed populations. Additionally, we performed PBS on real South Asian populations masked with local ancestry deconvolution and report here the first possible selection signals on the autochthonous South Asian component of contemporary South Asian populations.
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Affiliation(s)
- Burak Yelmen
- Institute of Genomics, University of Tartu, Estonia.,Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | | | - Ludovica Molinaro
- Institute of Genomics, University of Tartu, Estonia.,Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | | | | | - Luca Pagani
- Institute of Genomics, University of Tartu, Estonia.,Department of Biology, University of Padova, Italy
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35
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Morandi F, Marimpietri D, Görgens A, Gallo A, Srinivasan RC, El-Andaloussi S, Gramignoli R. Human Amnion Epithelial Cells Impair T Cell Proliferation: The Role of HLA-G and HLA-E Molecules. Cells 2020; 9:E2123. [PMID: 32961693 PMCID: PMC7563681 DOI: 10.3390/cells9092123] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 09/01/2020] [Accepted: 09/16/2020] [Indexed: 12/13/2022] Open
Abstract
The immunoprivilege status characteristic of human amnion epithelial cells (hAECs) has been recently highlighted in the context of xenogenic transplantation. However, the mechanism(s) involved in such regulatory functions have been so far only partially been clarified. Here, we have analyzed the expression of HLA-Ib molecules in isolated hAEC obtained from full term placentae. Moreover, we asked whether these molecules are involved in the immunoregulatory functions of hAEC. Human amnion-derived cells expressed surface HLA-G and HLA-F at high levels, whereas the commonly expressed HLA-E molecule has been measured at a very low level or null on freshly isolated cells. HLA-Ib molecules can be expressed as membrane-bound and soluble forms, and in all hAEC batches analyzed we measured high levels of sHLA-G and sHLA-E when hAEC were maintained in culture, and such a release was time-dependent. Moreover, HLA-G was present in extracellular vesicles (EVs) released by hAEC. hAEC suppressed T cell proliferation in vitro at different hAEC:T cell ratios, as previously reported. Moreover, inhibition of T cell proliferation was partially reverted by pretreating hAEC with anti-HLA-G, anti-HLA-E and anti-β2 microglobulin, thus suggesting that HLA-G and -E molecules are involved in hAEC-mediated suppression of T cell proliferation. Finally, either large-size EV (lsEV) or small-size EV (ssEV) derived from hAEC significantly modulated T-cell proliferation. In conclusion, we have here characterized one of the mechanism(s) underlying immunomodulatory functions of hAEC, related to the expression and release of HLA-Ib molecules.
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Affiliation(s)
- Fabio Morandi
- Stem Cell Laboratory and Cell Therapy Center, IRCCS Istituto Giannina Gaslini, Via Gaslini5, 16147 Genova, Italy;
| | - Danilo Marimpietri
- Stem Cell Laboratory and Cell Therapy Center, IRCCS Istituto Giannina Gaslini, Via Gaslini5, 16147 Genova, Italy;
| | - Andre Görgens
- Department of Laboratory Medicine, Division of Biomolecular and Cellular Medicine, Karolinska Institutet, 14157 Stockholm, Sweden; (A.G.); (S.E.-A.)
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Alessia Gallo
- Department of Research, IRCCS ISMETT (Istituto Mediterraneo per i Trapianti e Terapie ad alta specializzazione), Via E.Tricomi 5, 90127 Palermo, Italy;
| | - Raghuraman Chittor Srinivasan
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Alfred Nobels Alle 8, Huddinge SE-141 83, 14157 Stockholm, Sweden;
| | - Samir El-Andaloussi
- Department of Laboratory Medicine, Division of Biomolecular and Cellular Medicine, Karolinska Institutet, 14157 Stockholm, Sweden; (A.G.); (S.E.-A.)
| | - Roberto Gramignoli
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Alfred Nobels Alle 8, Huddinge SE-141 83, 14157 Stockholm, Sweden;
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Wyatt RC, Lanzoni G, Russell MA, Gerling I, Richardson SJ. What the HLA-I!-Classical and Non-classical HLA Class I and Their Potential Roles in Type 1 Diabetes. Curr Diab Rep 2019; 19:159. [PMID: 31820163 PMCID: PMC6901423 DOI: 10.1007/s11892-019-1245-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
PURPOSE OF REVIEW Hyperexpression of classical HLA class I (HLA-I) molecules in insulin-containing islets has become a widely accepted hallmark of type 1 diabetes pathology. In comparison, relatively little is known about the expression, function and role of non-classical subtypes of HLA-I. This review focuses on the current understanding of the non-classical HLA-I subtypes: HLA-E, HLA-F and HLA-G, within and outside the field of type 1 diabetes, and considers the possible impacts of these molecules on disease etiology. RECENT FINDINGS Evidence is growing to suggest that non-classical HLA-I proteins are upregulated, both at the RNA and protein levels in the pancreas of individuals with recent-onset type 1 diabetes. Moreover, associations between non-classical HLA-I genotypes and age at onset of type 1 diabetes have been reported in some studies. As with classical HLA-I, it is likely that hyperexpression of non-classical HLA-I is driven by the release of diffusible interferons by stressed β cells (potentially driven by viral infection) and exacerbated by release of cytokines from infiltrating immune cells. Non-classical HLA-I proteins predominantly (but not exclusively) transduce negative signals to immune cells infiltrating at the site of injury/inflammation. We propose a model in which the islet endocrine cells, through expression of non-classical HLA-I are fighting back against the infiltrating immune cells. By inhibiting the activity and function on NK, B and select T cells, the non-classical HLA-I, proteins will reduce the non-specific bystander effects of inflammation, while at the same time still allowing the targeted destruction of β cells by specific islet-reactive CD8+ T cells.
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Affiliation(s)
- Rebecca C. Wyatt
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Building, Barrack Road, Exeter, EX2 5DW UK
| | - Giacomo Lanzoni
- Diabetes Research Institute, University of Miami – Miller School of Medicine, 1450 NW 10th Avenue, Miami, FL 33136 USA
- Department of Biochemistry and Molecular Biology, University of Miami – Miller School of Medicine, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Mark A. Russell
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Building, Barrack Road, Exeter, EX2 5DW UK
| | - Ivan Gerling
- Department of Medicine University of Tennessee Health Science Center and VA Medical Center Research Service, 1030 Jefferson Avenue, Memphis, TN 38128 USA
| | - Sarah J. Richardson
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Building, Barrack Road, Exeter, EX2 5DW UK
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Shiina T, Blancher A. The Cynomolgus Macaque MHC Polymorphism in Experimental Medicine. Cells 2019; 8:E978. [PMID: 31455025 PMCID: PMC6770713 DOI: 10.3390/cells8090978] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/20/2019] [Accepted: 08/22/2019] [Indexed: 02/07/2023] Open
Abstract
Among the non-human primates used in experimental medicine, cynomolgus macaques (Macaca fascicularis hereafter referred to as Mafa) are increasingly selected for the ease with which they are maintained and bred in captivity. Macaques belong to Old World monkeys and are phylogenetically much closer to humans than rodents, which are still the most frequently used animal model. Our understanding of the Mafa genome has progressed rapidly in recent years and has greatly benefited from the latest technical advances in molecular genetics. Cynomolgus macaques are widespread in Southeast Asia and numerous studies have shown a distinct genetic differentiation of continental and island populations. The major histocompatibility complex of cynomolgus macaque (Mafa MHC) is organized in the same way as that of human, but it differs from the latter by its high degree of classical class I gene duplication. Human polymorphic MHC regions play a pivotal role in allograft transplantation and have been associated with more than 100 diseases and/or phenotypes. The Mafa MHC polymorphism similarly plays a crucial role in experimental allografts of organs and stem cells. Experimental results show that the Mafa MHC class I and II regions influence the ability to mount an immune response against infectious pathogens and vaccines. MHC also affects cynomolgus macaque reproduction and impacts on numerous biological parameters. This review describes the Mafa MHC polymorphism and the methods currently used to characterize it. We discuss some of the major areas of experimental medicine where an effect induced by MHC polymorphism has been demonstrated.
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Affiliation(s)
- Takashi Shiina
- Department of Molecular Life Sciences, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Antoine Blancher
- Centre de Physiopathologie Toulouse-Purpan (CPTP), Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (Inserm), Université Paul Sabatier (UPS), Toulouse 31000, France.
- Laboratoire d'immunologie, CHU de Toulouse, Institut Fédératif de Biologie, hôpital Purpan, 330 Avenue de Grande Bretagne, TSA40031, 31059 Toulouse CEDEX 9, France.
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Lucar O, Reeves RK, Jost S. A Natural Impact: NK Cells at the Intersection of Cancer and HIV Disease. Front Immunol 2019; 10:1850. [PMID: 31474977 PMCID: PMC6705184 DOI: 10.3389/fimmu.2019.01850] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 07/23/2019] [Indexed: 12/24/2022] Open
Abstract
Despite efficient suppression of plasma viremia in people living with HIV (PLWH) on cART, evidence of HIV-induced immunosuppression remains, and normally benign and opportunistic pathogens become major sources of co-morbidities, including virus-induced cancers. In fact, cancer remains a primary cause of death even in virally suppressed PLWH. Natural killer (NK) cells provide rapid early responses to HIV infection, contribute substantially to disease modulation and vaccine protection, and are also major therapeutic targets for cancer immunotherapy. However, much like other lymphocyte populations, recent burgeoning evidence suggests that in chronic conditions like HIV, NK cells can become functionally exhausted with impaired cytotoxic function, altered cytokine production and impaired antibody-dependent cell-mediated cytotoxicity. Recent work suggests functional anergy is likely due to low-level ongoing virus replication, increased inflammatory cytokines, or increased presence of MHClow target cells. Indeed, HIV-induced loss of NK cell-mediated control of lytic EBV infection has been specifically shown to cause lymphoma and also increases replication of CMV. In this review, we will discuss current understanding of NK cell modulation of HIV disease, reciprocal exhaustion of NK cells, and how this may impact increased cancer incidences and prospects for NK cell-targeted immunotherapies. Finally, we will review the most recent evidence supporting adaptive functions of NK cells and highlight the potential of adaptive NK cells for cancer immunotherapy.
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Affiliation(s)
- Olivier Lucar
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - R Keith Reeves
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States.,Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, MA, United States
| | - Stephanie Jost
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
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