1
|
Sarani H, Molashahi B, Taheri M, Bahari G, Hashemi SM, Hashemi M, Ghavami S. Association between the Interleukin-1 Receptor Antagonist (IL1RN) Variable Number of Tandem Repeats (VNTR) Polymorphism and Lymphoma. Int J Hematol Oncol Stem Cell Res 2021; 15:90-95. [PMID: 34466207 PMCID: PMC8381109 DOI: 10.18502/ijhoscr.v15i2.6039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 05/05/2020] [Accepted: 09/17/2020] [Indexed: 12/24/2022] Open
Abstract
Introduction: Lymphoma is a common hematopoietic cancer. Immunosuppression is one of the main risk factors for the development of lymphoma. The interleukin (IL)-1 receptor antagonist IL1RN, which binds to the IL-1 receptor, moderates a variety of immune responses related to IL-1. We aimed to assess the impact of IL1RN variable number of tandem repeats (VNTR) polymorphism on lymphoma risk in an Iranian population sample. Materials and Methods: DNA was extracted from peripheral blood of 120 subjects with non-Hodgkin Lymphoma (NHL), 50 subjects with Hodgkin's lymphoma (HL), and 186 unrelated healthy individuals. IL1RN VNTR polymorphism was detected using polymerase chain reaction. Results: Our findings revealed that the IL1RN VNTR polymorphism was associated with protection against NHL (P≤0.001, OR: 0.30, 95% CI: 0.18-0.53). The IL1RN 2 allele significantly decreased the risk of NHL (p = 0.023, OR = 0.66, 95%CI = 0.46-0.93). In addition, we found that IL1RN 1/2 was associated with a lower risk of HL (p ≤0.001, OR = 0.24, 95%CI = 0.12-0.50). Conclusion: Our results suggest that the presence of IL1RN VNTR polymorphism is associated with a decreased risk of lymphoma in an Iranian subpopulation in southeast Iran.
Collapse
Affiliation(s)
- Hosna Sarani
- Genetics of Non-communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran.,Children and Adolescent Health Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Behrouz Molashahi
- Genetics of Non-communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mohsen Taheri
- Genetics of Non-communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran.,Department of Genetic, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Gholamreza Bahari
- Children and Adolescent Health Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Seyed Mahdi Hashemi
- Department of Internal Medicine, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mohammad Hashemi
- Genetics of Non-communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Saeid Ghavami
- Department of Human Anatomy and Cell Science, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| |
Collapse
|
2
|
Maeda S, Hijikata M, Hang NTL, Thuong PH, Huan HV, Hoang NP, Hung NV, Cuong VC, Miyabayashi A, Seto S, Keicho N. Genotyping of Mycobacterium tuberculosis spreading in Hanoi, Vietnam using conventional and whole genome sequencing methods. Infect Genet Evol 2020; 78:104107. [PMID: 31706080 DOI: 10.1016/j.meegid.2019.104107] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/24/2019] [Accepted: 11/04/2019] [Indexed: 12/22/2022]
Abstract
Hanoi is the capital of Vietnam, one of the 30 countries with a high tuberculosis (TB) burden. Fundamental data on the molecular epidemiology of the disease is required for future TB management. To identify lineages and genotypes of Mycobacterium tuberculosis (Mtb), conventional genotyping data from clinical isolates of the Hanoi area was compared with whole genome sequencing (WGS) analysis from 332 of 470 samples. It was obtained from lineage-specific single nucleotide variants (SNVs), large sequence polymorphisms, spoligotyping, and variable number of tandem repeats (VNTR) analysis using mycobacterial interspersed repetitive unit (MIRU) and Japan anti-tuberculosis association (JATA) locus sets. This information was directly compared with results obtained from WGS. Mini-satellite repeat unit variants were identified using BLAST search against concatenated short read sequences, the RepUnitTyping tool. WGS analysis revealed that the Mtb strains tested are diverse and classified into lineage (L) 1, 2 and 4 (24.7, 57.2 and 18.1% respectively). The majority of the L2 strains were further divided into ancient and modern Beijing genotypes, and most of the L1 group were EAI4_VNM strains. Although conventional PCR-based genotyping results were mostly consistent with information obtained through WGS analysis, in-depth analysis identified aberrant deletions and spacers that may cause discordance. JATA-VNTR sets, including hypervariable loci, separated large Beijing genotypic clusters generated by MIRU15 into smaller groups. The distribution of repeat unit variants observed within 33 VNTR loci showed clear variation depending on the three lineages. WGS-based pairwise-SNV differences within VNTR-defined genotypic clusters were greater in L1 than in L2 and L4 (P = .001). Direct comparisons between results of PCR-based genotyping and in silico analysis of WGS data would bridge a gap between classical and modern technologies during this transition period, and provide further information on Mtb genotypes in specific geographical areas.
Collapse
|
3
|
Wang B, Nyunt MH, Yun SG, Lu F, Cheng Y, Han JH, Ha KS, Park WS, Hong SH, Lim CS, Cao J, Sattabongkot J, Kyaw MP, Cui L, Han ET. Variable number of tandem repeats of 9 Plasmodium vivax genes among Southeast Asian isolates. Acta Trop 2017; 170:161-168. [PMID: 28119047 DOI: 10.1016/j.actatropica.2017.01.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 06/21/2016] [Revised: 01/12/2017] [Accepted: 01/16/2017] [Indexed: 02/01/2023]
Abstract
The variable number of tandem repeats (VNTRs) provides valuable information about both the functional and evolutionary aspects of genetic diversity. Comparative analysis of 3 Plasmodium falciparum genomes has shown that more than 9% of its open reading frames (ORFs) harbor VNTRs. Although microsatellites and VNTR genes of P. vivax were reported, the VNTR polymorphism of genes has not been examined widely. In this study, 230 P. vivax genes were analyzed for VNTRs by SERV, and 33 kinds of TR deletions or insertions from 29 P. vivax genes (12.6%) were found. Of these, 9 VNTR fragments from 8 P. vivax genes were used for PCR amplification and sequence analysis to examine the genetic diversity among 134 isolates from four Southeast Asian countries (China, Republic of Korea, Thailand, and Myanmar) with different malaria endemicity. We confirmed the existence of extensive polymorphism of VNTR fragments in field isolates. This detection provides several suitable markers for analysis of the molecular epidemiology of P. vivax field isolates.
Collapse
Affiliation(s)
- Bo Wang
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do 200-701, Republic of Korea; Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People's Republic of China
| | - Myat Htut Nyunt
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do 200-701, Republic of Korea; Department of Medical Research, Yangon 11191, Myanmar
| | - Seung-Gyu Yun
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul 152-703, Republic of Korea
| | - Feng Lu
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do 200-701, Republic of Korea; Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu 214064, People's Republic of China
| | - Yang Cheng
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do 200-701, Republic of Korea; Laboratory of Pathogen Infection and Immunity, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Jin-Hee Han
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do 200-701, Republic of Korea
| | - Kwon-Soo Ha
- Department of Molecular and Cellular Biochemistry, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do 200-701, Republic of Korea
| | - Won Sun Park
- Department of Physiology, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do 200-701, Republic of Korea
| | - Seok-Ho Hong
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do 200-701, Republic of Korea
| | - Chae-Seung Lim
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul 152-703, Republic of Korea
| | - Jun Cao
- Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu 214064, People's Republic of China
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | | | - Liwang Cui
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA
| | - Eun-Taek Han
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do 200-701, Republic of Korea.
| |
Collapse
|