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Wang X, Zhang Q, Hou S, Qi J, Du L, Li F, Cao Q, Yang P. Association of Long Non-coding RNA C1RL-AS1 and PTPN6 Gene Polymorphisms with Ocular Behcet's Disease in Han Chinese. Ocul Immunol Inflamm 2024; 32:336-341. [PMID: 36745681 DOI: 10.1080/09273948.2023.2170887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 11/15/2022] [Accepted: 01/16/2023] [Indexed: 02/07/2023]
Abstract
PURPOSE To explore the association of the polymorphisms in PTPN6 and LncRNA C1RL-AS1 genes with ocular BD in Han Chinese patients. METHODS Correlation study was performed using the iPLEX system on a cohort of ocular BD patients andcontrols. The genotyping of 7 SNPs for LncRNA C1RL-AS1 and PTPN6 genes in ocular BD patients was performed using the iPLEX Gold genotype. RESULTS The frequencies of rs4013722 AG genotype/A allele in LncRNA C1RL-AS1 were significantly decreased in BD patients, and the frequency of GG genotype was significantly increased in BD patients. The rs4013722 was associated with ocular BD in male patients, but not in female patients. The AG and GG genotype of rs4013722 were associated with skin lesions in male patients. The gene polymorphisms of PTPN6 were not associated with BD patients. CONCLUSIONS The LncRNA C1RL-AS1/rs4013722 polymorphism conferred susceptibility to ocular BD in Han Chinese patients, which was influenced by sex.Abbreviations: LncRNA: Long Non-coding RNA; BD: Behcet's disease; SNP: single nucleotide polymorphism; PBMCs: peripheral blood mononuclear cells; PTPs: Protein tyrosine phosphatases; PTPN6: protein tyrosine phosphatase non-receptor 6; GWAS: genome-wide association study; HWE: Hardy-Weinberg equilibrium; LD: linkage disequilibrium; OR: odds ratio; CI: confidence interval; eQTL: expression quantitative trait loci; IBD: inflammatory bowel disease; RA: rheumatoid arthritis; Padj: Bonferroni corrected P value; NS: non-significant.
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Affiliation(s)
- Xiaotang Wang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipal Division) of National Clinical Research Center for Ocular Diseases, Chongqing, People's Republic of China
| | - Qi Zhang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipal Division) of National Clinical Research Center for Ocular Diseases, Chongqing, People's Republic of China
| | - Shengping Hou
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipal Division) of National Clinical Research Center for Ocular Diseases, Chongqing, People's Republic of China
| | - Jian Qi
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipal Division) of National Clinical Research Center for Ocular Diseases, Chongqing, People's Republic of China
| | - Liping Du
- Department of Ophthalmology, the First Affiliated Hospital of Zhengzhou University, Henan Province Eye Hospital, Henan International Joint Research Laboratory for Ocular Immunology and Retinal Injury Repair, Zhengzhou, People's Republic of China
| | - Fuzhen Li
- Department of Ophthalmology, the First Affiliated Hospital of Zhengzhou University, Henan Province Eye Hospital, Henan International Joint Research Laboratory for Ocular Immunology and Retinal Injury Repair, Zhengzhou, People's Republic of China
| | - Qingfeng Cao
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipal Division) of National Clinical Research Center for Ocular Diseases, Chongqing, People's Republic of China
| | - Peizeng Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch (Municipal Division) of National Clinical Research Center for Ocular Diseases, Chongqing, People's Republic of China
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Li H, Zheng P, Li Z, Han Q, Zhou B, Wang K. C-type lectin 2D (CLEC2D) is upregulated in clear cell renal cell carcinoma (ccRCC) tissues and predicts poor prognosis. Heliyon 2024; 10:e27354. [PMID: 38509909 PMCID: PMC10950488 DOI: 10.1016/j.heliyon.2024.e27354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is known as the most common type of renal cancer. Recently, a series of advances have been made in targeted therapy for ccRCC. To combat this highly metastatic tumor, novel therapeutic targets still need to be developed. C-type lectins (CLECs) contain a characteristic C-type lectin-like domain and affect several physiological functions. The effects of C-type lectin 2D (CLEC2D) on cancer progression have been revealed in several types of cancers; however, its expression in ccRCC tissues, and the possible effects on the progression and metastasis of ccRCC, are still unclear. Herein, we found the high mRNA and protein levels of CLEC2D in ccRCC tissues. We further found that CLEC2D expression was correlated with the prognosis of ccRCC patients and correlated with the tumor size (p = 0.019*) of patients. In addition, CLEC2D affected tumor immune infiltration, confirmed by the further analysis. CLEC2D knockdown suppressed the proliferation of ccRCC cells in vitro and restrained ccRCC tumor growth and immune infiltration in mice. Therefore, we believe that CLEC2D has the potential to serve as a promising ccRCC therapeutic target.
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Affiliation(s)
- Huibing Li
- Department of Urology, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471003, China
| | - Pengyi Zheng
- Department of Urology, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471003, China
| | - Zhijun Li
- Department of Urology, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471003, China
| | - Qingjiang Han
- Department of Urology, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471003, China
| | - Bisheng Zhou
- Department of Urology, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471003, China
| | - Kaixuan Wang
- Department of Urology, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, 471003, China
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Pan X, Muk T, Ren S, Nguyen DN, Shen RL, Gao F, Sangild PT. Blood transcriptomic markers of necrotizing enterocolitis in preterm pigs. Pediatr Res 2022; 91:1113-1120. [PMID: 34112973 DOI: 10.1038/s41390-021-01605-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 04/29/2021] [Accepted: 05/24/2021] [Indexed: 12/25/2022]
Abstract
BACKGROUND Necrotizing enterocolitis (NEC), a severe gut disorder in preterm infants, is difficult to predict due to poor specificity and sensitivity of clinical signs and biomarkers. Using preterm piglets as a model, we hypothesized that early development of NEC affects blood gene expression, potentially related to early systemic immune responses. METHODS A retrospective analysis of clinical, tissue, and blood data was performed on 129 formula-fed piglets with NEC diagnosis at necropsy on day 5. Subgroups of NEC (n = 20) and control piglets (CON, n = 19) were analyzed for whole-blood transcriptome. RESULTS Preterm piglets had variable NEC lesions, especially in the colon region, without severe clinical signs (e.g. normal growth, activity, hematology, digestion, few piglets with bloody stools). Transcriptome analysis showed 344 differentially expressed genes (DEGs) between NEC and CON piglets. Validation experiment showed that AOAH, ARG2, FKBP5, PAK2, and STAT3 were among the genes affected by severe lesions on day 5, when analyzed in whole blood and in dried blood spots (DBS). CONCLUSION Whole-blood gene expressions may be affected in preterm pigs before clinical signs of NEC get severe. Blood gene expression analysis, potentially using DBS samples, is a novel tool to help identify new early biomarkers of NEC. IMPACT Preterm pig model was used to investigate if blood transcriptomics could be used to identify new early blood biomarkers of NEC progression. Whole-blood transcriptome revealed upregulation of target genes in NEC cases when clinical symptoms are subtle, and mainly colon regions were affected. Differential NEC-associated gene expressions could be detected also in dried blood spots, potentially allowing easy collection of small blood volumes in infants.
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Affiliation(s)
- Xiaoyu Pan
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tik Muk
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Shuqiang Ren
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Duc Ninh Nguyen
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rene L Shen
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Fei Gao
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Per Torp Sangild
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,H.C. Andersen Childrens Hospital, Odense University Hospital, University of Southern Denmark, Odense, Denmark. .,Department of Neonatology, Rigshospitalet, Copenhagen, Denmark.
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4
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Hurkmans DP, Basak EA, Schepers N, Oomen-De Hoop E, Van der Leest CH, El Bouazzaoui S, Bins S, Koolen SLW, Sleijfer S, Van der Veldt AAM, Debets R, Van Schaik RHN, Aerts JGJV, Mathijssen RHJ. Granzyme B is correlated with clinical outcome after PD-1 blockade in patients with stage IV non-small-cell lung cancer. J Immunother Cancer 2021; 8:jitc-2020-000586. [PMID: 32461348 PMCID: PMC7254154 DOI: 10.1136/jitc-2020-000586] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2020] [Indexed: 01/05/2023] Open
Abstract
Background A minority of patients with advanced non-small-cell lung cancer (NSCLC) benefit from treatment with immune checkpoint inhibitors (ICIs). Ineffective effector function of activated T and NK cells may lead to reduced tumor cell death, even when these activated effector cells are released from their immune checkpoint brake. Hence, in this study we aimed to assess the association of baseline serum granzyme B, as well as germline variation of the GZMB gene, with clinical outcome to programmed cell death protein 1 (PD-1) blockade. Methods A total of 347 patients with stage IV NSCLC who started nivolumab treatment between June 2013 and June 2017 were prospectively included. Baseline serum and whole blood was available, allowing for protein quantification and targeted DNA sequencing. Clinical outcome was based on best overall response (BOR) according to Response Evaluation Criteria in Solid Tumors, V.1.1, progression-free survival (PFS), and overall survival (OS). Results Patients with low serum levels of granzyme B had worse PFS (HR: 1.96; 95% CI: 1.12 to 3.43; p=0.018) and worse OS (HR: 2.08; 95% CI: 1.12 to 3.87; p=0.021) than patients with high baseline serum levels. To validate the findings, germline variation of GZMB rs8192917 was assessed. Patients with homozygous and heterozygous variants of GZMB rs8192917 had worse BOR (OR: 1.60; 95% CI: 1.01 to 2.52; p=0.044) and worse PFS (HR: 1.38; 95% CI:1.02 to 1.87; p=0.036) than wild types. Conclusions A low baseline serum level of granzyme B and germline variation of GZMB was associated with worse clinical outcome in NSCLC, emphasizing the relevance and additional value of monitoring germline genetic variations which mirror cytotoxic functions of T cells in ICI therapy. Trail registration number Dutch Trial Registry (NL6828).
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Affiliation(s)
- Daan P Hurkmans
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands .,Department of Pulmonology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Edwin A Basak
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Nina Schepers
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Esther Oomen-De Hoop
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | | | - Samira El Bouazzaoui
- Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sander Bins
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Stijn L W Koolen
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.,Departmemt of Hospital Pharmacy, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Astrid A M Van der Veldt
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.,Department of Radiology & Nuclear Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Reno Debets
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Ron H N Van Schaik
- Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joachim G J V Aerts
- Department of Pulmonology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ron H J Mathijssen
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
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Kent A, Longino NV, Christians A, Davila E. Naturally Occurring Genetic Alterations in Proximal TCR Signaling and Implications for Cancer Immunotherapy. Front Immunol 2021; 12:658611. [PMID: 34012443 PMCID: PMC8126620 DOI: 10.3389/fimmu.2021.658611] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
T cell-based immunotherapies including genetically engineered T cells, adoptive transfer of tumor-infiltrating lymphocytes, and immune checkpoint blockade highlight the impressive anti-tumor effects of T cells. These successes have provided new hope to many cancer patients with otherwise poor prognoses. However, only a fraction of patients demonstrates durable responses to these forms of therapies and many develop significant immune-mediated toxicity. These heterogeneous clinical responses suggest that underlying nuances in T cell genetics, phenotypes, and activation states likely modulate the therapeutic impact of these approaches. To better characterize known genetic variations that may impact T cell function, we 1) review the function of early T cell receptor-specific signaling mediators, 2) offer a synopsis of known mutations and genetic alterations within the associated molecules, 3) discuss the link between these mutations and human disease and 4) review therapeutic strategies under development or in clinical testing that target each of these molecules for enhancing anti-tumor T cell activity. Finally, we discuss novel engineering approaches that could be designed based on our understanding of the function of these molecules in health and disease.
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Affiliation(s)
- Andrew Kent
- Division of Medical Oncology, Department of Medicine, University of Colorado, Aurora, CO, United States
- Human Immunology and Immunotherapy Initiative, University of Colorado, Aurora, CO, United States
- University of Colorado Comprehensive Cancer Center, Aurora, CO, United States
| | - Natalie V. Longino
- Division of Medical Oncology, Department of Medicine, University of Colorado, Aurora, CO, United States
- Human Immunology and Immunotherapy Initiative, University of Colorado, Aurora, CO, United States
- University of Colorado Comprehensive Cancer Center, Aurora, CO, United States
- Department of Medicine, University of Colorado, Aurora, CO, United States
| | - Allison Christians
- Division of Medical Oncology, Department of Medicine, University of Colorado, Aurora, CO, United States
- Human Immunology and Immunotherapy Initiative, University of Colorado, Aurora, CO, United States
- University of Colorado Comprehensive Cancer Center, Aurora, CO, United States
| | - Eduardo Davila
- Division of Medical Oncology, Department of Medicine, University of Colorado, Aurora, CO, United States
- Human Immunology and Immunotherapy Initiative, University of Colorado, Aurora, CO, United States
- University of Colorado Comprehensive Cancer Center, Aurora, CO, United States
- Department of Medicine, University of Colorado, Aurora, CO, United States
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6
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de With M, Hurkmans DP, Oomen-de Hoop E, Lalouti A, Bins S, El Bouazzaoui S, van Brakel M, Debets R, Aerts JGJV, van Schaik RHN, Mathijssen RHJ, van der Veldt AAM. Germline Variation in PDCD1 Is Associated with Overall Survival in Patients with Metastatic Melanoma Treated with Anti-PD-1 Monotherapy. Cancers (Basel) 2021; 13:cancers13061370. [PMID: 33803602 PMCID: PMC8002987 DOI: 10.3390/cancers13061370] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/06/2021] [Accepted: 03/15/2021] [Indexed: 01/14/2023] Open
Abstract
A substantial number of melanoma patients do not benefit from therapy with anti-PD-1. Therefore, we investigated the predictive value of single nucleotide polymorphisms (SNPs) in genes related to the PD-1 axis in patients with metastatic melanoma. From 119 consecutive melanoma patients who were treated with pembrolizumab or nivolumab monotherapy, blood samples were genotyped for 11 SNPs in nine genes. Associations between SNPs and OS were tested using Cox regression analysis and internally validated by bootstrapping. For SNPs with a statistical significance, an expression quantitative trait loci (eQTL) analysis was performed. In a subset of patients, immunophenotyping was performed. Patients with a SNP in PDCD1 (804C > T; rs2227981) had a significantly poorer OS with a 3-year OS rate of 51.8%, as compared to 71% in wild type patients (hazard ratio [HR] 2.37; 95% CI: 1.11-5.04; p = 0.026). eQTL analysis showed that this SNP was associated with decreased gene expression. In addition, PDCD1 804C > T carriers had a reduced fraction of peripheral PD-1+CD4+ T cells. No other associations between SNPs and OS were found. PDCD1 804C > T is associated with poorer OS after anti-PD-1 monotherapy in patients with metastatic melanoma. This SNP may affect clinical benefit from ICIs by decreasing transcription initiation and expression of PD-1 in T cells.
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Affiliation(s)
- Mirjam de With
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (M.d.W.); (E.O.-d.H.); (A.L.); (S.B.); (M.v.B.); (R.D.); (R.H.J.M.); (A.A.M.v.d.V.)
- Department of Clinical Chemistry, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (S.E.B.); (R.H.N.v.S.)
| | - Daan P. Hurkmans
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (M.d.W.); (E.O.-d.H.); (A.L.); (S.B.); (M.v.B.); (R.D.); (R.H.J.M.); (A.A.M.v.d.V.)
- Department of Pulmonology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands;
- Correspondence: ; Tel.: +31-10-704-11-12
| | - Esther Oomen-de Hoop
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (M.d.W.); (E.O.-d.H.); (A.L.); (S.B.); (M.v.B.); (R.D.); (R.H.J.M.); (A.A.M.v.d.V.)
| | - Ayoub Lalouti
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (M.d.W.); (E.O.-d.H.); (A.L.); (S.B.); (M.v.B.); (R.D.); (R.H.J.M.); (A.A.M.v.d.V.)
| | - Sander Bins
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (M.d.W.); (E.O.-d.H.); (A.L.); (S.B.); (M.v.B.); (R.D.); (R.H.J.M.); (A.A.M.v.d.V.)
| | - Samira El Bouazzaoui
- Department of Clinical Chemistry, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (S.E.B.); (R.H.N.v.S.)
| | - Mandy van Brakel
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (M.d.W.); (E.O.-d.H.); (A.L.); (S.B.); (M.v.B.); (R.D.); (R.H.J.M.); (A.A.M.v.d.V.)
| | - Reno Debets
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (M.d.W.); (E.O.-d.H.); (A.L.); (S.B.); (M.v.B.); (R.D.); (R.H.J.M.); (A.A.M.v.d.V.)
| | - Joachim G. J. V. Aerts
- Department of Pulmonology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands;
| | - Ron H. N. van Schaik
- Department of Clinical Chemistry, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (S.E.B.); (R.H.N.v.S.)
| | - Ron H. J. Mathijssen
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (M.d.W.); (E.O.-d.H.); (A.L.); (S.B.); (M.v.B.); (R.D.); (R.H.J.M.); (A.A.M.v.d.V.)
| | - Astrid A. M. van der Veldt
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (M.d.W.); (E.O.-d.H.); (A.L.); (S.B.); (M.v.B.); (R.D.); (R.H.J.M.); (A.A.M.v.d.V.)
- Department of Radiology & Nuclear Medicine, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands
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Rahmani F, Rayzan E, Rahmani MR, Shahkarami S, Zoghi S, Rezaei A, Aryan Z, Najafi M, Rohlfs M, Jeske T, Aflatoonian M, Chavoshzadeh Z, Farahmand F, Motamed F, Rohani P, Alimadadi H, Mahdaviani A, Mansouri M, Tavakol M, Vanderberg M, Kotlarz D, Klein C, Rezaei N. Clinical and Mutation Description of the First Iranian Cohort of Infantile Inflammatory Bowel Disease: The Iranian Primary Immunodeficiency Registry (IPIDR). Immunol Invest 2020; 50:445-459. [PMID: 32633164 DOI: 10.1080/08820139.2020.1776725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We describe a cohort of 25 Iranian patients with infantile inflammatory bowel disease (IBD), 14 (56%) of whom had monogenic defects. After proper screening, patients were referred for whole exome sequencing (WES). Four patients had missense mutations in the IL10 RA, and one had a large deletion in the IL10 RB. Four patients had mutations in genes implicated in host:microbiome homeostasis, including TTC7A deficiency, and two patients with novel mutations in the TTC37 and NOX1. We found a novel homozygous mutation in the SRP54 in a deceased patient and the heterozygous variant in his sibling with a milder phenotype. Three patients had combined immunodeficiency: one with ZAP-70 deficiency (T+B+NK-), and two with atypical SCID due to mutations in RAG1 and LIG4. One patient had a G6PC3 mutation without neutropenia. Eleven of the 14 patients with monogenic defects were results of consanguinity and only 4 of them were alive to this date.
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Affiliation(s)
- Farzaneh Rahmani
- Department of Radiology, Washington University School of Medicine, St Louis, Missouri, USA.,Student's Scientific Research Center, Tehran University of Medical Sciences (TUMS), Tehran, Iran.,NeuroImaging Network (NIN), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Elham Rayzan
- International Hematology/Oncology of Pediatrics' Experts (IHOPE), Universal Scientific Education and Research Network (USERN), Tehran, Iran.,Research Center for Immunodeficiencies (RCID), Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Rahmani
- Department of Immunology & Hematology, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Sepideh Shahkarami
- Medical Genetics Network (Megene), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Samaneh Zoghi
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Arezoo Rezaei
- Research Center for Immunodeficiencies (RCID), Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Aryan
- Research Center for Immunodeficiencies (RCID), Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehri Najafi
- Department of Gastroenterology, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Meino Rohlfs
- Department of Pediatrics, Dr. Von Hauner Children's Hospital, Ludwig Maximilians University, Munich, Germany
| | - Tim Jeske
- Department of Pediatrics, Dr. Von Hauner Children's Hospital, Ludwig Maximilians University, Munich, Germany
| | - Majid Aflatoonian
- Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Chavoshzadeh
- Pediatric Infectious Research Center, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Farahmand
- Department of Gastroenterology, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Farzaneh Motamed
- Department of Gastroenterology, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Pejman Rohani
- Pediatric Gastroenterology, Hepatology and Nutrition Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Alimadadi
- Department of Gastroenterology, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Mahdaviani
- Pediatric Congenital Hematologic Disorders Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahboubeh Mansouri
- Immunology and Allergy Department, Mofid Children Hospital, Shahid Behehshti University of Medical Sciences, Tehran, Iran
| | - Marzieh Tavakol
- Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Mirjam Vanderberg
- Laboratory for Immunology, Dept. Of Pediatrics, Leiden University Medical Center, Netherlands
| | - Daniel Kotlarz
- Department of Pediatrics, Dr. Von Hauner Children's Hospital, Ludwig Maximilians University, Munich, Germany
| | - Christoph Klein
- Department of Pediatrics, Dr. Von Hauner Children's Hospital, Ludwig Maximilians University, Munich, Germany
| | - Nima Rezaei
- Research Center for Immunodeficiencies (RCID), Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
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Kelsen JR, Sullivan KE, Rabizadeh S, Singh N, Snapper S, Elkadri A, Grossman AB. North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition Position Paper on the Evaluation and Management for Patients With Very Early-onset Inflammatory Bowel Disease. J Pediatr Gastroenterol Nutr 2020; 70:389-403. [PMID: 32079889 DOI: 10.1097/mpg.0000000000002567] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The rate of pediatric inflammatory bowel disease (IBD) has been increasing over the last decade and this increase has occurred most rapidly in the youngest children diagnosed <6 years, known as very early-onset inflammatory bowel disease (VEO-IBD). These children can present with more extensive and severe disease than older children and adults. The contribution of host genetics in this population is underscored by the young age of onset and the distinct, aggressive phenotype. In fact, monogenic defects, often involving primary immunodeficiency genes, have been identified in children with VEO-IBD and have led to targeted and life-saving therapy. This position paper will discuss the phenotype of VEO-IBD and outline the approach and evaluation for these children and what factors should trigger concern for an underlying immunodeficiency. We will then review the immunological assays and genetic studies that can facilitate the identification of the underlying diagnosis in patients with VEO-IBD and how this evaluation may lead to directed therapies. The position paper will also aid the pediatric gastroenterologist in recognizing when a patient should be referred to a center specializing in the care of these patients. These guidelines are intended for pediatricians, allied health professionals caring for children, pediatric gastroenterologists, pediatric pathologists, and immunologists.
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Affiliation(s)
| | - Kathleen E Sullivan
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Shervin Rabizadeh
- Division of Gastroenterology, Hepatology, and Nutrition, Cedar-Sinai Medical Center, Los Angeles, CA
| | - Namita Singh
- Division of Gastroenterology, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA
| | - Scott Snapper
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School
- Division of Gastroenterology, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA
| | - Abdul Elkadri
- Division of Gastroenterology, Hepatology, and Nutrition, Medical College of Wisconsin, Milwaukee, WI
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Abstract
Protein tyrosine phosphatases (PTPs) play a critical role in co-ordinating the signaling networks that maintain lymphocyte homeostasis and direct lymphocyte activation. By dephosphorylating tyrosine residues, PTPs have been shown to modulate enzyme activity and both mediate and disrupt protein-protein interactions. Through these molecular mechanisms, PTPs ultimately impact lymphocyte responses to environmental cues such as inflammatory cytokines and chemokines, as well as antigenic stimulation. Mouse models of acute and chronic intestinal inflammation have been shown to be exacerbated in the absence of PTPs such as PTPN2 and PTPN22. This increase in disease severity is due in part to hyper-activation of lymphocytes in the absence of PTP activity. In accordance, human PTPs have been linked to intestinal inflammation. Genome wide association studies (GWAS) identified several PTPs within risk loci for inflammatory bowel disease (IBD). Therapeutically targeting PTP substrates and their associated signaling pathways, such as those implicated in CD4+ T cell responses, has demonstrated clinical efficacy. The current review focuses on the role of PTPs in controlling CD4+ T cell activity in the intestinal mucosa and how disruption of PTP activity in CD4+ T cells can contribute to intestinal inflammation.
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Affiliation(s)
- Kelly A Pike
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada.,Inception Sciences Canada, Montréal, QC, Canada
| | - Michel L Tremblay
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada.,Rosalind and Morris Goodman Cancer Centre, McGill University, Montréal, QC, Canada.,Division of Experimental Medicine, Department of Medicine, McGill University, Montréal, QC, Canada.,Department of Biochemistry, McGill University, Montréal, QC, Canada
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Bins S, Basak EA, El Bouazzaoui S, Koolen SLW, Oomen-de Hoop E, van der Leest CH, van der Veldt AAM, Sleijfer S, Debets R, van Schaik RHN, Aerts JGJV, Mathijssen RHJ. Association between single-nucleotide polymorphisms and adverse events in nivolumab-treated non-small cell lung cancer patients. Br J Cancer. 2018;118:1296-1301. [PMID: 29695768 PMCID: PMC5959881 DOI: 10.1038/s41416-018-0074-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 03/09/2018] [Accepted: 03/13/2018] [Indexed: 02/08/2023] Open
Abstract
Background Treatment with PD-1 inhibitors can be hampered by severe auto-immune-related toxicities. Our objective was to identify single-nucleotide polymorphisms (SNPs) in genes previously associated with auto-immunity, which are associated with toxicities in nivolumab-treated NSCLC patients. This was in order to identify patients prone to develop severe toxicities and to gain more insight into the underlying pathobiology. Methods We analysed 322 nivolumab-treated patients and assessed the association with toxicities for seven SNPs in four genes, which are considered contributors to PD-1-directed T-cell responses, i.e., PDCD1, PTPN11, ZAP70 and IFNG. Every SNP was tested for its association with toxicity endpoints. Significant associations were tested in a validation cohort. Results A multivariable analysis in the exploration cohort showed that homozygous variant patients for PDCD1 804C>T (rs2227981) had decreased odds for any grade treatment-related toxicities (n = 96; OR 0.4; 95% CI 0.2–1.0; p = 0.039). However, this result could not be validated (n = 85; OR 0.9; 95% CI 0.4–1.9; p = NS). Conclusions Our results show that it is unlikely that the investigated SNPs have a clinical implication in predicting toxicity. A finding, even though negative, that is considered timely and instructive towards further research in biomarker development for checkpoint inhibitor treatments.
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Yuan F, Zhang YH, Kong XY, Cai YD. Identification of Candidate Genes Related to Inflammatory Bowel Disease Using Minimum Redundancy Maximum Relevance, Incremental Feature Selection, and the Shortest-Path Approach. Biomed Res Int. 2017;2017:5741948. [PMID: 28293637 PMCID: PMC5331171 DOI: 10.1155/2017/5741948] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 01/11/2017] [Indexed: 02/08/2023]
Abstract
Identification of disease genes is a hot topic in biomedicine and genomics. However, it is a challenging problem because of the complexity of diseases. Inflammatory bowel disease (IBD) is an idiopathic disease caused by a dysregulated immune response to host intestinal microflora. It has been proven to be associated with the development of intestinal malignancies. Although the specific pathological characteristics and genetic background of IBD have been partially revealed, it is still an overdetermined disease and the blueprint of all genetic variants still needs to be improved. In this study, a novel computational method was built to identify genes related to IBD. Samples from two subtypes of IBD (ulcerative colitis and Crohn's disease) and normal samples were employed. By analyzing the gene expression profiles of these samples using minimum redundancy maximum relevance and incremental feature selection, 21 genes were obtained that could effectively distinguish samples from the two subtypes of IBD and the normal samples. Then, the shortest-path approach was used to search for an additional 20 genes in a large network constructed using protein-protein interactions based on the above-mentioned 21 genes. Analyses of the 41 genes obtained indicate that they are closely associated with this disease.
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Spalinger MR, McCole DF, Rogler G, Scharl M. Role of protein tyrosine phosphatases in regulating the immune system: implications for chronic intestinal inflammation. Inflamm Bowel Dis 2015; 21:645-55. [PMID: 25581833 DOI: 10.1097/MIB.0000000000000297] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Current hypothesis suggests that genetic, immunological, and bacterial factors contribute essentially to the pathogenesis of inflammatory bowel disease. Variations within the gene loci encoding protein tyrosine phosphatases (PTPs) have been associated with the onset of inflammatory bowel disease. PTPs modulate the activity of their substrates by dephosphorylation of tyrosine residues and are critical for the regulation of fundamental cellular signaling processes. Evidence emerges that expression levels of PTPN2, PTPN11, and PTPN22 are altered in actively inflamed intestinal tissue. PTPN2 seems to be critical for protecting intestinal epithelial barrier function, regulating innate and adaptive immune responses and finally for maintaining intestinal homeostasis. These observations have been confirmed in PTPN2 knockout mice in vivo. Those animals are clearly more susceptible to intestinal and systemic inflammation and feature alterations in innate and adaptive immune responses. PTPN22 controls inflammatory signaling in lymphocytes and mononuclear cells resulting in aberrant cytokine secretion pattern and autophagosome formation. PTPN22 deficiency in vivo results in more severe colitis demonstrating the relevance of PTPN22 for intestinal homeostasis in vivo. Of note, loss of PTPN22 promotes mitogen-activated protein kinase-induced cytokine secretion but limits secretion of nuclear factor κB-associated cytokines and autophagy in mononuclear cells. Loss of PTPN11 is also associated with increased colitis severity in vivo. In summary, dysfunction of those PTPs results in aberrant and uncontrolled immune responses that result in chronic inflammatory conditions. This way, it becomes more and more evident that dysfunction of PTPs displays an important factor in the pathogenesis of chronic intestinal inflammation, in particular inflammatory bowel disease.
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Ferjeni Z, Bouzid D, Fourati H, Stayoussef M, Abida O, Kammoun T, Hachicha M, Penha-Gonçalves C, Masmoudi H. Association of TCR/CD3, PTPN22, CD28 and ZAP70 gene polymorphisms with type 1 diabetes risk in Tunisian population: family based association study. Immunol Lett 2014; 163:1-7. [PMID: 25448703 DOI: 10.1016/j.imlet.2014.11.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 10/30/2014] [Accepted: 11/10/2014] [Indexed: 11/28/2022]
Abstract
Type 1 diabetes (T1D) is caused by an immune-mediated destruction of the insulin-producing β-cells. Several studies support the involvement of T cell activation molecules in the pathogenesis of T1D. In order to underline the role of the genes involved in this activation pathway, we investigated, using the Sequenom MassARRAY platform, 45 single-nucleotide polymorphisms (SNPs) belonging to TCR/CD3, CD28, ZAP70, and PTPN22 genes in 59 T1D Tunisian families. In the current study, we identified an association with rs706 (Z score=2.782; p=0.005) of TCRβ gene. We also demonstrated that rs10918706 in the intron of the CD3z gene was associated with increased risk of T1D (Z score 2.137; p=0.032). In the same region, rs2949655 (Z score=2.101; p=0.035) and rs1214611 (Z score=4.036; p=0.00005) showed a genotype association with the risk of T1D. When haplotypes were constructed, GAA haplotype displayed significant association with T1D (Z score=2.135; p=0.032), while GGA haplotype (Z score=-1.988; p=0.046) was negatively associated with the disease. We also identified an association with rs3181096 (Z score=2.177; p=0.029), rs17695937 (Z score =2.111; p=0.034) and rs2488457 (Z score=2.219; p=0.026), respectively of CD28, ZAP70 and PTPN22 genes. In addition, our results suggest a significant effect on T1D susceptibility for AC (Z score=2.30; p=0.02) and CTGGC (Z score=2.309, p=0.02) haplotypes of ZAP70 and PTPN22 genes, respectively. While, the GTCT (Z score=-2.114, p=0.034) and CTAGG (Z score=-2.121, p=0.033) haplotypes of CD28 and PTPN22 genes, may confer protection against T1D. These findings confirm the role of PTPN22 and CD28 involved in the T cell activation pathway in the development of T1D in Tunisian families. Interestingly, ZAP70 and TCRβ/CD3z seem to contribute to the susceptibility to the disease in our population. However, this finding has to be confirmed in further studies.
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Affiliation(s)
- Zouidi Ferjeni
- Immunology Department, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia.
| | - D Bouzid
- Immunology Department, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - H Fourati
- Immunology Department, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - M Stayoussef
- Immunology Department, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - O Abida
- Immunology Department, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
| | - T Kammoun
- Pediatric Department, Hedi Chaker Hospital, University of Sfax, Sfax, Tunisia
| | - M Hachicha
- Pediatric Department, Hedi Chaker Hospital, University of Sfax, Sfax, Tunisia
| | | | - H Masmoudi
- Immunology Department, Habib Bourguiba Hospital, University of Sfax, Sfax, Tunisia
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Zouidi F, Stayoussef M, Bouzid D, Fourati H, Abida O, Ayed MB, Kammoun T, Hachicha M, Penha-gonçalves C, Masmoudi H. Contribution of PTPN22, CD28, CTLA-4 and ZAP-70 variants to the risk of type 1 diabetes in Tunisians. Gene 2014; 533:420-6. [DOI: 10.1016/j.gene.2013.09.112] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 09/25/2013] [Accepted: 09/27/2013] [Indexed: 01/27/2023]
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