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Lin J, Shen M, Xiao W, Chen Y, Yu S, Meng Y. Common and rare variants in genetic susceptibility analysis of mature B-cell neoplasm subtypes by whole exome sequencing. Leukemia 2024; 38:2059-2063. [PMID: 38965369 DOI: 10.1038/s41375-024-02332-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/23/2024] [Accepted: 06/27/2024] [Indexed: 07/06/2024]
Affiliation(s)
- Junwei Lin
- Guangzhou KingMed Transformative Medicine Institute Co. Ltd, Guangzhou, China
- KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, China
| | - Maoting Shen
- Guangzhou KingMed Transformative Medicine Institute Co. Ltd, Guangzhou, China
- KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, China
| | - Wenjuan Xiao
- Guangzhou Kingmylab Pharmaceutical Research Co. Ltd, Guangzhou, China
| | - Yuxin Chen
- Guangzhou KingMed Diagnostics Group Co. Ltd, Guangzhou, China
| | - Shihui Yu
- KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, China
- Guangzhou KingMed Diagnostics Group Co. Ltd, Guangzhou, China
| | - Yuhuan Meng
- Guangzhou KingMed Transformative Medicine Institute Co. Ltd, Guangzhou, China.
- KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, China.
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Thomsen H, Chattopadhyay S, Weinhold N, Vodicka P, Vodickova L, Hoffmann P, Nöthen MM, Jöckel KH, Schmidt B, Hajek R, Hallmans G, Pettersson-Kymmer U, Späth F, Goldschmidt H, Hemminki K, Försti A. Haplotype analysis identifies functional elements in monoclonal gammopathy of unknown significance. Blood Cancer J 2024; 14:140. [PMID: 39164264 PMCID: PMC11335940 DOI: 10.1038/s41408-024-01121-8] [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: 05/22/2024] [Revised: 08/02/2024] [Accepted: 08/06/2024] [Indexed: 08/22/2024] Open
Abstract
Genome-wide association studies (GWASs) based on common single nucleotide polymorphisms (SNPs) have identified several loci associated with the risk of monoclonal gammopathy of unknown significance (MGUS), a precursor condition for multiple myeloma (MM). We hypothesized that analyzing haplotypes might be more useful than analyzing individual SNPs, as it could identify functional chromosomal units that collectively contribute to MGUS risk. To test this hypothesis, we used data from our previous GWAS on 992 MGUS cases and 2910 controls from three European populations. We identified 23 haplotypes that were associated with the risk of MGUS at the genome-wide significance level (p < 5 × 10-8) and showed consistent results among all three populations. In 10 genomic regions, strong promoter, enhancer and regulatory element-related histone marks and their connections to target genes as well as genome segmentation data supported the importance of these regions in MGUS susceptibility. Several associated haplotypes affected pathways important for MM cell survival such as ubiquitin-proteasome system (RNF186, OTUD3), PI3K/AKT/mTOR (HINT3), innate immunity (SEC14L1, ZBP1), cell death regulation (BID) and NOTCH signaling (RBPJ). These pathways are important current therapeutic targets for MM, which may highlight the advantage of the haplotype approach homing to functional units.
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Affiliation(s)
- Hauke Thomsen
- MSB Medical School Berlin, Hochschule für Gesundheit und Medizin, Berlin, Germany
| | - Subhayan Chattopadhyay
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Niels Weinhold
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Pavel Vodicka
- Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, Pilsen, Czech Republic
| | - Ludmila Vodickova
- Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Prague, Czech Republic
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, Pilsen, Czech Republic
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Börge Schmidt
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Roman Hajek
- Department of Hematooncology, University Hospital Ostrava and Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - Göran Hallmans
- Department of Public Health and Clinical Medicine, Umea University, Umea, Sweden
| | - Ulrika Pettersson-Kymmer
- Clinical Pharmacology, Department of Pharmacology and Clinical Neuroscience, Umea University, Umea, Sweden
| | - Florentin Späth
- Department of Diagnostics and Intervention, Cancer Center, Hematology, Umeå University, Umeå, Sweden
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
- National Centre of Tumor Diseases, Heidelberg, Germany
| | - Kari Hemminki
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, Pilsen, Czech Republic
- Department of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Asta Försti
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany.
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Pudjihartono N, Ho D, O’Sullivan JM. Integrative analysis reveals novel insights into juvenile idiopathic arthritis pathogenesis and shared molecular pathways with associated traits. Front Genet 2024; 15:1448363. [PMID: 39175752 PMCID: PMC11338781 DOI: 10.3389/fgene.2024.1448363] [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: 06/13/2024] [Accepted: 07/22/2024] [Indexed: 08/24/2024] Open
Abstract
Background Juvenile idiopathic arthritis (JIA) is an autoimmune joint disease that frequently co-occurs with other complex phenotypes, including cancers and other autoimmune diseases. Despite the identification of numerous risk variants through genome-wide association studies (GWAS), the affected genes, their connection to JIA pathogenesis, and their role in the development of associated traits remain unclear. This study aims to address these gaps by elucidating the gene-regulatory mechanisms underlying JIA pathogenesis and exploring its potential role in the emergence of associated traits. Methods A two-sample Mendelian Randomization (MR) analysis was conducted to identify blood-expressed genes causally linked to JIA. A curated protein interaction network was subsequently used to identify sets of single-nucleotide polymorphisms (i.e., spatial eQTL SNPs) that regulate the expression of JIA causal genes and their protein interaction partners. These SNPs were cross-referenced against the GWAS catalog to identify statistically enriched traits associated with JIA. Results The two-sample MR analysis identified 52 genes whose expression changes in the blood are putatively causal for JIA. These genes (e.g., HLA, LTA, LTB, IL6ST) participate in a range of immune-related pathways (e.g., antigen presentation, cytokine signalling) and demonstrate cell type-specific regulatory patterns across different immune cell types (e.g., PPP1R11 in CD4+ T cells). The spatial eQTLs that regulate JIA causal genes and their interaction partners were statistically enriched for GWAS SNPs linked with 95 other traits, including both known and novel JIA-associated traits. This integrative analysis identified genes whose dysregulation may explain the links between JIA and associated traits, such as autoimmune/inflammatory diseases (genes at 6p22.1 locus), Hodgkin lymphoma (genes at 6p21.3 [FKBPL, PBX2, AGER]), and chronic lymphocytic leukemia (BAK1). Conclusion Our approach provides a significant advance in understanding the genetic architecture of JIA and associated traits. The results suggest that the burden of associated traits may differ among JIA patients, influenced by their combined genetic risk across different clusters of traits. Future experimental validation of the identified connections could pave the way for refined patient stratification, the discovery of new biomarkers, and shared therapeutic targets.
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Affiliation(s)
- N. Pudjihartono
- The Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - D. Ho
- The Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - J. M. O’Sullivan
- The Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, United Kingdom
- Australian Parkinsons Mission, Garvan Institute of Medical Research, Sydney, NSW, Australia
- A*STAR Singapore Institute for Clinical Sciences, Singapore, Singapore
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Svyatova G, Berezina G, Bazarbayeva A, Omarova K, Kussainov A. Genetic Markers of Acute Childhood B-Lineage Lymphoblastic Leukemia in the Kazakh Population. Fetal Pediatr Pathol 2024:1-15. [PMID: 38989811 DOI: 10.1080/15513815.2024.2375523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 06/27/2024] [Indexed: 07/12/2024]
Abstract
INTRODUCTION To investigate the genetic contribution of 24 GWAS-associated polymorphic gene variants on the development of children's B-lineage acute lymphoblastic leukemia (B-ALL) in an ethnically homogeneous population of Kazakhs. METHODS A study of 205 children with B-ALL and 204 healthy children was conducted. Genotyping of polymorphic loci was carried out using the TaqMan method. RESULTS Significant associations (p < 0.05) with the risk of childhood B-ALL were found for twelve variants, including rs6457327 of the HLA gene, rs4251961 of the IL1RN gene, and rs1800630 of the TNF gene. Carriage of the minor allele A of the protective rs1801157 polymorphism A of the CXCL12 gene reduces the risk of B-ALL in the Kazakh population by 40%. DISCUSSION The results reveal significant associations of polymorphic genetic variants, which can serve as a basis for the development of effective methods for predicting the risk of B-ALL, early diagnosis, and timely treatment.
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Affiliation(s)
- Gulnara Svyatova
- Department of the Republican Medical Genetic Consultation, Scientific Center for Obstetrics, Gynecology and Perinatology, Almaty, Republic of Kazakhstan
| | - Galina Berezina
- Department of the Republican Medical Genetic Consultation, Scientific Center for Obstetrics, Gynecology and Perinatology, Almaty, Republic of Kazakhstan
| | - Aigul Bazarbayeva
- Department of Science and Education, Scientific Center of Pediatric and Children's Surgery, Almaty, Republic of Kazakhstan
| | - Kulyan Omarova
- Department of Science and Education, Scientific Center of Pediatric and Children's Surgery, Almaty, Republic of Kazakhstan
| | - Abay Kussainov
- Scientific Center of Pediatric and Children's Surgery, Almaty, Republic of Kazakhstan
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Reeve MP, Vehviläinen M, Luo S, Ritari J, Karjalainen J, Gracia-Tabuenca J, Mehtonen J, Padmanabhuni SS, Kolosov N, Artomov M, Siirtola H, Olilla HM, Graham D, Partanen J, Xavier RJ, Daly MJ, Ripatti S, Salo T, Siponen M. Oral and non-oral lichen planus show genetic heterogeneity and differential risk for autoimmune disease and oral cancer. Am J Hum Genet 2024; 111:1047-1060. [PMID: 38776927 PMCID: PMC11179409 DOI: 10.1016/j.ajhg.2024.04.020] [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: 02/29/2024] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024] Open
Abstract
Lichen planus (LP) is a T-cell-mediated inflammatory disease affecting squamous epithelia in many parts of the body, most often the skin and oral mucosa. Cutaneous LP is usually transient and oral LP (OLP) is most often chronic, so we performed a large-scale genetic and epidemiological study of LP to address whether the oral and non-oral subgroups have shared or distinct underlying pathologies and their overlap with autoimmune disease. Using lifelong records covering diagnoses, procedures, and clinic identity from 473,580 individuals in the FinnGen study, genome-wide association analyses were conducted on carefully constructed subcategories of OLP (n = 3,323) and non-oral LP (n = 4,356) and on the combined group. We identified 15 genome-wide significant associations in FinnGen and an additional 12 when meta-analyzed with UKBB (27 independent associations at 25 distinct genomic locations), most of which are shared between oral and non-oral LP. Many associations coincide with known autoimmune disease loci, consistent with the epidemiologic enrichment of LP with hypothyroidism and other autoimmune diseases. Notably, a third of the FinnGen associations demonstrate significant differences between OLP and non-OLP. We also observed a 13.6-fold risk for tongue cancer and an elevated risk for other oral cancers in OLP, in agreement with earlier reports that connect LP with higher cancer incidence. In addition to a large-scale dissection of LP genetics and comorbidities, our study demonstrates the use of comprehensive, multidimensional health registry data to address outstanding clinical questions and reveal underlying biological mechanisms in common but understudied diseases.
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Affiliation(s)
- Mary Pat Reeve
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Mari Vehviläinen
- Department of Oral and Maxillofacial Diseases, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Shuang Luo
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Jarmo Ritari
- Finnish Red Cross Blood Service, Helsinki, Finland
| | - Juha Karjalainen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Javier Gracia-Tabuenca
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Juha Mehtonen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Shanmukha Sampath Padmanabhuni
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Nikita Kolosov
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland; Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Ohio State University College of Medicine, Columbus, OH, USA
| | - Mykyta Artomov
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland; Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Ohio State University College of Medicine, Columbus, OH, USA
| | - Harri Siirtola
- TAUCHI Research Center, Tampere University, Tampere, Finland
| | - Hanna M Olilla
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Daniel Graham
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mark J Daly
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytical and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Tuula Salo
- Research Unit of Population Health, Department of Oral Pathology, University of Oulu and Oulu University Hospital, Oulu, Finland; Medical Research Center, Oulu University Hospital, Oulu, Finland; Department of Oral and Maxillofacial Diseases, and Translational Immunology Program (TRIMM), University of Helsinki, Helsinki, Finland
| | - Maria Siponen
- Institute of Dentistry, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland; Odontology Education Unit, and Oral and Maxillofacial Diseases Clinic, Kuopio University Hospital, Kuopio, Finland
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Diamanti I, Fylaktou A, Verrou E, Vlachaki E, Sinakos M, Katodritou E, Ouranos K, Minti F, Gioula G. HLA variations in patients with diffuse large B-cell lymphoma and association with disease risk and prognosis: a case-control study. Front Genet 2024; 15:1341822. [PMID: 38680423 PMCID: PMC11045888 DOI: 10.3389/fgene.2024.1341822] [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: 11/22/2023] [Accepted: 03/27/2024] [Indexed: 05/01/2024] Open
Abstract
Introduction Human leukocyte antigen (HLA) polymorphisms have been associated with the development of various autoimmune diseases, as well as malignant neoplasms. Non-Hodgkin lymphomas (NHLs) are a heterogenous group of lymphoid malignancies in which a genetic substrate has been established and is deemed to play a crucial role in disease pathogenesis. This study aimed to identify whether variations in the HLA gene region were associated with diffuse large B-cell lymphoma (DLBCL) risk and prognosis. Methods We defined HLA class I (HLA-A, HLA-B, HLA-C) and class II (HLA-DRB1, HLA-DQB1) alleles in 60 patients with DLBCL and compared the results to those found by 236 healthy adult donors from the bone marrow bank of Northern Greece. HLA typing was performed by two molecular methods, Sequence - Specific Oligonucleotide HLA typing (SSO) and Sequence - Specific Primer HLA typing (SSP), from white blood cells recovered from peripheral blood. The phenotypic frequencies of HLA-A, HLA-B, HLA-C, HLA-DRB1 and HLA-DQB1 between patients and controls were compared with the 2-sided Fisher's exact test. Results with p-value <0.05 were considered statistically significant. Odds Ratios with 95% Confidence Intervals were calculated to further strengthen the results. The 2-sided Fisher's exact test was also applied to alleles found only in one of the two groups, while the odds ratios together with the confidence intervals were corrected with Haldane-Anscombe method. Results Among the studied HLA polymorphisms, the frequency HLA-C*12 allele was significantly lower in patients with DLBCL compared with control subjects (6.7% vs. 34.7%, OR = 0.16, 95% CI: 0.04-0.44). Frequency of HLA-B*39 was significantly lower in patients with DLBCL compared with controls, but due to the low frequency of this polymorphism in the studied population and small sample size, determinations regarding the significance of this findings were limited. Survival analysis revealed that the presence of HLA-C*12 was not associated with improved or worsened overall and progression-free survival. No statistically significant associations were observed in the phenotypic frequencies of HLA-A, HLA-DQB1, HLA-DRB1 and the rest of HLA-B alleles between the control and DLBCL groups. Discussion Collectively, our results provide valuable insight regarding the role of HLA variations on DLBCL risk. Further studies are required to consolidate our findings and ascertain the clinical implications of these genetic variations on DLBCL management and prognosis.
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Affiliation(s)
- Ioanna Diamanti
- Biochemisty and Microbiology Department, Theagenio Cancer Hospital, Thessaloniki, Greece
| | - Asimina Fylaktou
- National Peripheral Histocompatibility Center-Immunology Department, Hippokration General Hospital, Thessaloniki, Greece
| | - Evgenia Verrou
- Hematology Department, Theagenio Cancer Hospital, Thessaloniki, Greece
| | - Efthimia Vlachaki
- Thalassemia Unit-2nd Department of Internal Medicine, Hippokration General Hospital, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Manolis Sinakos
- 4th Department of Internal Medicine, Hippokration General Hospital, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Eirini Katodritou
- Hematology Department, Theagenio Cancer Hospital, Thessaloniki, Greece
| | - Konstantinos Ouranos
- Department of Medicine, Houston Methodist Research Institute, Houston, TX, United States
| | - Fani Minti
- Microbiology Department, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Georgia Gioula
- Microbiology Department, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Li YM, Li YX, Li DY, Zhou Y, An L, Yuan ZY, Du KM, Zheng ZZ. Investigation of HLA susceptibility alleles and genotypes with hematological disease among Chinese Han population. PLoS One 2024; 19:e0281698. [PMID: 38593173 PMCID: PMC11003630 DOI: 10.1371/journal.pone.0281698] [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: 01/29/2023] [Accepted: 02/10/2024] [Indexed: 04/11/2024] Open
Abstract
Several genes involved in the pathogenesis have been identified, with the human leukocyte antigen (HLA) system playing an essential role. However, the relationship between HLA and a cluster of hematological diseases has received little attention in China. Blood samples (n = 123913) from 43568 patients and 80345 individuals without known pathology were genotyped for HLA class I and II using sequencing-based typing. We discovered that HLA-A*11:01, B*40:01, C*01:02, DQB1*03:01, and DRB1*09:01 were prevalent in China. Furthermore, three high-frequency alleles (DQB1*03:01, DQB1*06:02, and DRB1*15:01) were found to be hazardous in malignant hematologic diseases when compared to controls. In addition, for benign hematologic disorders, 7 high-frequency risk alleles (A*01:01, B*46:01, C*01:02, DQB1*03:03, DQB1*05:02, DRB1*09:01, and DRB1*14:54) and 8 high-frequency susceptible genotypes (A*11:01-A*11:01, B*46:01-B*58:01, B*46:01-B*46:01, C*01:02-C*03:04, DQB1*03:01-DQB1*05:02, DQB1*03:03-DQB1*06:01, DRB1*09:01-DRB1*15:01, and DRB1*14:54-DRB1*15:01) were observed. To summarize, our findings indicate the association between HLA alleles/genotypes and a variety of hematological disorders, which is critical for disease surveillance.
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Affiliation(s)
- Ye-Mo Li
- Shenzhen Tissuebank Precision Medicine Co., Ltd, Shenzhen, China
| | - Yu-Xia Li
- Shanghai Tissuebank Biotechnology Co., Ltd, Shanghai, China
| | - Dai-Yang Li
- Shenzhen Tissuebank Precision Medicine Co., Ltd, Shenzhen, China
| | - Ying Zhou
- Shenzhen Tissuebank Precision Medicine Co., Ltd, Shenzhen, China
| | - Lin An
- Shanghai Tissuebank Biotechnology Co., Ltd, Shanghai, China
| | - Zhi-Yang Yuan
- Shenzhen Tissuebank Precision Medicine Co., Ltd, Shenzhen, China
| | - Ke-Ming Du
- Shenzhen Tissuebank Precision Medicine Co., Ltd, Shenzhen, China
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Tizu M, Calenic B, Hârza M, Cristea BM, Maruntelu I, Caragea AM, Talangescu A, Dima A, Constantinescu AE, Constantinescu I. HLA Gene Polymorphisms in Romanian Patients with Chronic Lymphocytic Leukemia. Genet Res (Camb) 2024; 2024:8852876. [PMID: 38449839 PMCID: PMC10917483 DOI: 10.1155/2024/8852876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/24/2023] [Accepted: 02/21/2024] [Indexed: 03/08/2024] Open
Abstract
Materials and Methods This study included 66 patients with CLL, diagnosed between 2020 and 2022, and 100 healthy controls. HLA class I and class II genes (HLA-A/B/C, HLA-DQA1/DQB1/DPA1/DPB1, and HLA-DRB1/3/4/5) were investigated using next-generation sequencing technology. Results Several HLA alleles were strongly associated with CLL. The most important finding was that HLA-DRB1∗04:02:01 (p=0.001, OR = 1.05) and HLA-DRB3∗02:01:01 (p=0.009, OR = 1.03) have a predisposing role in CLL development. Moreover, we identified that HLA-A∗24:02:01 0.01 (p=0.01, OR = 0.38), HLA-DQA1∗05:05:01 (p=0.01, OR = 0.56), HLA-DQB1∗03:02:01 (p=0.03, OR = 0.40), and HLA-DRB4∗01:03:01 (p=0.03, OR = 0.54 alleles have protective roles. Correlations between HLA expression and gender showed that women had a higher expression of protective HLA alleles when compared to men. Conclusions Our data are the first to indicate that in Romanian patients with CLL, the HLA-A∗24:02:01 and HLA-DQA1∗05:05:01 alleles have a protective role against CLL development, whereas HLA-DRB1∗04:02:01 and HLA-DRB3∗02:01:01alleles are positively associated with CLL.
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Affiliation(s)
- Maria Tizu
- Immunology and Transplant Immunology, Carol Davila University of Medicine and Pharmacy, 258 Fundeni Avenue, Bucharest 022328, Romania
- Centre of Immunogenetics and Virology, Fundeni Clinical Institute, 258 Fundeni Avenue, Bucharest 022328, Romania
| | - Bogdan Calenic
- Immunology and Transplant Immunology, Carol Davila University of Medicine and Pharmacy, 258 Fundeni Avenue, Bucharest 022328, Romania
| | - Mihai Hârza
- Immunology and Transplant Immunology, Carol Davila University of Medicine and Pharmacy, 258 Fundeni Avenue, Bucharest 022328, Romania
- Centre of Immunogenetics and Virology, Fundeni Clinical Institute, 258 Fundeni Avenue, Bucharest 022328, Romania
| | - Bogdan M. Cristea
- Immunology and Transplant Immunology, Carol Davila University of Medicine and Pharmacy, 258 Fundeni Avenue, Bucharest 022328, Romania
| | - Ion Maruntelu
- Centre of Immunogenetics and Virology, Fundeni Clinical Institute, 258 Fundeni Avenue, Bucharest 022328, Romania
| | - Andreea M. Caragea
- Immunology and Transplant Immunology, Carol Davila University of Medicine and Pharmacy, 258 Fundeni Avenue, Bucharest 022328, Romania
| | - Adriana Talangescu
- Centre of Immunogenetics and Virology, Fundeni Clinical Institute, 258 Fundeni Avenue, Bucharest 022328, Romania
| | - Alina Dima
- Colentina Clinical Hospital, Rheumatology Department Bucharest, 19-21 Stefan Cel Mare Street, Bucharest 020125, Romania
| | - Alexandra E. Constantinescu
- Immunology and Transplant Immunology, Carol Davila University of Medicine and Pharmacy, 258 Fundeni Avenue, Bucharest 022328, Romania
| | - Ileana Constantinescu
- Immunology and Transplant Immunology, Carol Davila University of Medicine and Pharmacy, 258 Fundeni Avenue, Bucharest 022328, Romania
- Centre of Immunogenetics and Virology, Fundeni Clinical Institute, 258 Fundeni Avenue, Bucharest 022328, Romania
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Tizu M, Calenic B, Maruntelu I, Caragea AM, Talangescu A, Ursu L, Rotarescu C, Surugiu M, Constantinescu AE, Constantinescu I. Immunogenetic Background of Chronic Lymphoproliferative Disorders in Romanian Patients-Case Control Study. Med Sci (Basel) 2024; 12:14. [PMID: 38535155 PMCID: PMC10972167 DOI: 10.3390/medsci12010014] [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: 12/05/2023] [Revised: 02/06/2024] [Accepted: 02/18/2024] [Indexed: 08/25/2024] Open
Abstract
BACKGROUND AND OBJECTIVES The implications of the genetic component in the initiation and development of chronic lymphoproliferative disorders have been the subject of intense research efforts. Some of the most important genes involved in the occurrence and evolution of these pathologies are the HLA genes. The aim of this study is to analyze, for the first time, possible associations between chronic lymphoproliferative diseases and certain HLA alleles in the Romanian population. MATERIALS AND METHODS This study included 38 patients with chronic lymphoproliferative disorders, diagnosed between 2021 and 2022 at Fundeni Clinical Institute, Bucharest, Romania, and 50 healthy controls. HLA class I and class II genes (HLA-A/B/C, HLA-DQB1/DPB1/DRB1) were investigated by doing high resolution genotyping using sequence specific primers (SSP). RESULTS Several HLA alleles were strongly associated with chronic lymphoproliferative disorders. The most important finding was that the HLA-C*02:02 (p = 0.002, OR = 1.101), and HLA-C*12:02 (p = 0.002, OR = 1.101) have a predisposing role in the development of chronic lymphoproliferative disorders. Moreover, we identified that HLA-A*11:01 (p = 0.01, OR = 0.16), HLA-B*35:02 (p = 0.037, OR = 0.94), HLA-B*81:01 (p = 0.037, OR = 0.94), HLA-C*07:02 (p = 0.036, OR = 0.34), HLA-DRB1*11:01 (p = 0.021, OR = 0.19), and HLA-DRB1*13:02 (p = 0.037, OR = 0.94), alleles have protective roles. CONCLUSIONS Our study indicates that HLA-C*02:02 and HLA-C*12:02 are positively associated with chronic lymphoproliferative disorders for our Romanian patients while HLA-DRB1*11:01, HLA-DRB1*13:02, and HLA-B*35:02 alleles have a protective role against these diseases.
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Affiliation(s)
- Maria Tizu
- Immunology and Transplant Immunology, Carol Davila University of Medicine and Pharmacy, 258 Fundeni Avenue, 022328 Bucharest, Romania; (B.C.); (C.R.)
- Centre of Immunogenetics and Virology, Fundeni Clinical Institute, 258 Fundeni Avenue, 022328 Bucharest, Romania (A.T.)
| | - Bogdan Calenic
- Immunology and Transplant Immunology, Carol Davila University of Medicine and Pharmacy, 258 Fundeni Avenue, 022328 Bucharest, Romania; (B.C.); (C.R.)
| | - Ion Maruntelu
- Centre of Immunogenetics and Virology, Fundeni Clinical Institute, 258 Fundeni Avenue, 022328 Bucharest, Romania (A.T.)
| | - Andreea Mirela Caragea
- Immunology and Transplant Immunology, Carol Davila University of Medicine and Pharmacy, 258 Fundeni Avenue, 022328 Bucharest, Romania; (B.C.); (C.R.)
- Centre of Immunogenetics and Virology, Fundeni Clinical Institute, 258 Fundeni Avenue, 022328 Bucharest, Romania (A.T.)
| | - Adriana Talangescu
- Centre of Immunogenetics and Virology, Fundeni Clinical Institute, 258 Fundeni Avenue, 022328 Bucharest, Romania (A.T.)
| | - Larisa Ursu
- Immunology and Transplant Immunology, Carol Davila University of Medicine and Pharmacy, 258 Fundeni Avenue, 022328 Bucharest, Romania; (B.C.); (C.R.)
| | - Corina Rotarescu
- Immunology and Transplant Immunology, Carol Davila University of Medicine and Pharmacy, 258 Fundeni Avenue, 022328 Bucharest, Romania; (B.C.); (C.R.)
| | - Mariana Surugiu
- Immunology and Transplant Immunology, Carol Davila University of Medicine and Pharmacy, 258 Fundeni Avenue, 022328 Bucharest, Romania; (B.C.); (C.R.)
| | - Alexandra Elena Constantinescu
- Immunology and Transplant Immunology, Carol Davila University of Medicine and Pharmacy, 258 Fundeni Avenue, 022328 Bucharest, Romania; (B.C.); (C.R.)
| | - Ileana Constantinescu
- Immunology and Transplant Immunology, Carol Davila University of Medicine and Pharmacy, 258 Fundeni Avenue, 022328 Bucharest, Romania; (B.C.); (C.R.)
- Centre of Immunogenetics and Virology, Fundeni Clinical Institute, 258 Fundeni Avenue, 022328 Bucharest, Romania (A.T.)
- Academy of Romanian Scientists (AOSR), 3 Ilfov Street, Sector 5, 022328 Bucharest, Romania
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10
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Shi X, Wallach JD, Ma X, Rogne T. Autoimmune diseases and risk of non-Hodgkin lymphoma: A Mendelian randomisation study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.20.24301459. [PMID: 38343812 PMCID: PMC10854352 DOI: 10.1101/2024.01.20.24301459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Objective To examine whether genetically predicted susceptibility to ten autoimmune diseases (Behçet's disease, coeliac disease, dermatitis herpetiformis, lupus, psoriasis, rheumatoid arthritis, sarcoidosis, Sjögren's syndrome, systemic sclerosis, and type 1 diabetes) is associated with risk of non-Hodgkin lymphoma (NHL). Design Two sample Mendelian randomization (MR) study. Setting Genome wide association studies (GWASs) of ten autoimmune diseases, NHL, and four NHL subtypes (i.e., follicular lymphoma, mature T/natural killer-cell lymphomas, non-follicular lymphoma, and other and unspecified types of NHL). Analysis We used data from the largest publicly available GWASs of European ancestry for each autoimmune disease, NHL, and NHL subtypes. For each autoimmune disease, we extracted single nucleotide polymorphisms (SNPs) strongly associated (P < 5×10-8) with that disease and that were independent of one another (R2 < 1×10-3) as genetic instruments. SNPs within the human leukocyte antigen region were not considered due to potential pleiotropy. Our primary MR analysis was the inverse-variance weighted analysis. Additionally, we conducted MR-Egger, weighted mode, and weighted median regression to address potential bias due to pleiotropy, and robust adjusted profile scores to address weak instrument bias. We carried out sensitivity analysis limited to the non-immune pathway for nominally significant findings. To account for multiple testing, we set the thresholds for statistical significance at P < 5×10-3. Participants The number of cases and controls identified in the relevant GWASs were 437 and 3,325 for Behçet's disease, 4,918 and 5,684 for coeliac disease, 435 and 341,188 for dermatitis herpetiformis, 4,576 and 8,039 for lupus, 11,988 and 275,335 for psoriasis, 22,350 and 74,823 for rheumatoid arthritis, 3,597 and 337,121 for sarcoidosis, 2,735 and 332,115 for Sjögren's syndrome, 9,095 and 17,584 for systemic sclerosis, 18,942 and 501,638 for type 1 diabetes, 2,400 and 410,350 for NHL; and 296 to 2,340 cases and 271,463 controls for NHL subtypes. Exposures Genetic variants predicting ten autoimmune diseases: Behçet's disease, coeliac disease, dermatitis herpetiformis, lupus, psoriasis, rheumatoid arthritis, sarcoidosis, Sjögren's syndrome, systemic sclerosis, and type 1 diabetes. Main outcome measures Estimated associations between genetically predicted susceptibility to ten autoimmune diseases and the risk of NHL. Results The variance of each autoimmune disease explained by the SNPs ranged from 0.3% to 3.1%. Negative associations between type 1 diabetes and sarcoidosis and the risk of NHL were observed (odds ratio [OR] 0.95, 95% confidence interval [CI]: 0.92 to 0.98, P = 5×10-3, and OR 0.92, 95% CI: 0.85 to 0.99, P = 2.8×10-2, respectively). These findings were supported by the sensitivity analyses accounting for potential pleiotropy and weak instrument bias. No significant associations were found between the other eight autoimmune diseases and NHL risk. Of the NHL subtypes, type 1 diabetes was most strongly associated with follicular lymphoma (OR 0.91, 95% CI: 0.86 to 0.96, P = 1×10-3), while sarcoidosis was most strongly associated with other and unspecified NHL (OR 0.86, 95% CI: 0.75 to 0.97, P = 1.8×10-2). Conclusions These findings suggest that genetically predicted susceptibility to type 1 diabetes, and to some extent sarcoidosis, might reduce the risk of NHL. However, future studies with different datasets, approaches, and populations are warranted to further examine the potential associations between these autoimmune diseases and the risk of NHL.
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Affiliation(s)
- Xiaoting Shi
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut, USA
- Yale Center for Perinatal, Pediatric, and Environmental Epidemiology, Yale School of Public Health, New Haven, Connecticut, USA
| | - Joshua D. Wallach
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Xiaomei Ma
- Department of Chronic Diseases Epidemiology, Yale School of Public Health, New Haven, Connecticut, USA
| | - Tormod Rogne
- Department of Chronic Diseases Epidemiology, Yale School of Public Health, New Haven, Connecticut, USA
- Yale Center for Perinatal, Pediatric, and Environmental Epidemiology, Yale School of Public Health, New Haven, Connecticut, USA
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11
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Wang SS. Epidemiology and etiology of diffuse large B-cell lymphoma. Semin Hematol 2023; 60:255-266. [PMID: 38242772 PMCID: PMC10962251 DOI: 10.1053/j.seminhematol.2023.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/15/2023] [Accepted: 11/21/2023] [Indexed: 01/21/2024]
Abstract
As the most common non-Hodgkin lymphoma subtype, diffuse large B-cell lymphoma (DLBCL) incidence patterns generally parallel that for NHL overall. Globally, DLBCL accounts for a third of all NHLs, ranging between 20% and 50% by country. Based on United States (U.S.) cancer registry data, age-standardized incidence rate for DLBCL was 7.2 per 100,000. DLBCL incidence rises with age and is generally higher in males than females; in the U.S., incidence is highest among non-Hispanic whites (9.2/100,000). Like NHL incidence, DLBCL incidence rose in the first half of the 20th century but has largely plateaued. However, there is some evidence that incidence rates are rising in areas of historically low rates, such as Asia; there are also estimates for rising DLBCL incidence in the near future due to the changing demographics in developed countries whose aging population is growing. Established risk factors for DLBCL include those that result in severe immune deficiency such as HIV/AIDS, inherited immunodeficiency syndromes, and organ transplant recipients. Factors that lead to chronic immune dysregulations are also established risk factors, and include a number of autoimmune conditions (eg, Sjögren syndrome, systemic lupus erythematosus, rheumatoid arthritis), viral infections (eg, HIV, KSHV/HHV8, HCV, EBV), and obesity. Family history of NHL/DLBCL, personal history of cancer, and multiple genetic susceptibility loci are also well-established risk factors for DLBCL. There is strong evidence for multiple environmental exposures in DLBCL etiology, including exposure to trichloroethylene, benzene, and pesticides and herbicides, with recent associations noted with glyphosate. There is also strong evidence for associations with other viruses, such as HBV. Recent estimates suggest that obesity accounts for nearly a quarter of DLBCLs that develop, but despite recent gains in the understanding of DLBCL etiology, the majority of disease remain unexplained. An understanding of the host and environmental contributions to disease etiology, and concerted efforts to expand our understanding to multiple race/ethnic groups, will be essential for constructing clinically relevant risk prediction models and develop effective strategies for disease prevention.
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Affiliation(s)
- Sophia S Wang
- City of Hope Comprehensive Cancer Center, Duarte, CA.
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12
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Chen N, Wang F, Zhao Y, Dong L, Wang W, Zhang W, He J, Zhu F. HLA-A*02:06 allele may be susceptible to myelodysplastic syndrome in Zhejiang Han population, China. Int J Immunogenet 2023; 50:233-242. [PMID: 37485595 DOI: 10.1111/iji.12629] [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: 02/11/2023] [Revised: 06/21/2023] [Accepted: 07/13/2023] [Indexed: 07/25/2023]
Abstract
The association between HLA loci and haematological malignancy has been reported in certain populations. However, there are limited data for HLA loci at a high-resolution level with haematological malignancy in China. In this study, a total of 1115 patients with haematological malignancies (including 490 AML, 410 acute lymphoblastic leukaemia (ALL), 122 myelodysplastic syndrome [MDS] and 93 non-Hodgkin's lymphoma [NHL]) and 1836 healthy individuals as a control group in the Han population of Zhejiang Province, China, were genotyped for HLA-A, HLA-C, HLA-B, HLA-DRB1 and HLA-DQB1 loci at high resolution. The possible association between HLA alleles and haplotypes and haematologic malignancy was analysed. The allele frequencies (AFs) of HLA-A*02:05, HLA-A*02:06, HLA-A*32:01, HLA-B*35:03, HLA-B*54:01, HLA-B*55:07, HLA-DRB1*04:05, HLA-DRB1*15:01, HLA-DQB1*04:01 and HLA-DQB1*06:02 in the MDS patients were much higher than those in the control group (P < 0.05), while the AFs of HLA-C*07:02, HLA-DRB1*03:01, HLA-DRB1*14:54, HLA-DQB1*02:01 and HLA-DQB1*05:03 were obviously lower than those in the control group (p < .05). Interestingly, the differences in these HLA alleles in patients with MDS were not significant after applying Bonferroni correction (Pc > .05), except for HLA-A*02:06 (Pc < .01). There were 13, 6 and 10 HLA alleles with uncorrected significant differences (p < .05) among patients with AML, ALL and NHL, respectively, compared with those in the control group, but the differences in these HLA alleles were not significant after correction (Pc > .05). Compared to those of the control group, there were some haplotypes over 1.00% frequency in patients with AML, MDS and NHL patients with uncorrected significant differences (p < .05). However, none of them showed a significant difference after correction as well (Pc > .05). The study reveals that HLA-A*02:06 may lead to susceptibility to MDS, but none of the HLA alleles were associated with AML, ALL or NHL after correction. These data will help to further understand the role of HLA loci in the pathogenesis of haematological malignancy in China.
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Affiliation(s)
- Nanying Chen
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
- HLA Typing Laboratory, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Fang Wang
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
- HLA Typing Laboratory, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Yanmin Zhao
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lina Dong
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
- HLA Typing Laboratory, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Wei Wang
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
- HLA Typing Laboratory, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Wei Zhang
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
- HLA Typing Laboratory, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Ji He
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
- HLA Typing Laboratory, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
| | - Faming Zhu
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, China
- HLA Typing Laboratory, Key Laboratory of Blood Safety Research of Zhejiang Province, Hangzhou, China
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13
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Sarani H, Mollashahi B, Taheri M, Bahari G, Hashemi SM, Hashemi M, Ghavami S. Association between the IL-1A, IL-1B and IL-1R polymorphisms and lymphoma. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2021; 40:707-719. [PMID: 34159887 DOI: 10.1080/15257770.2021.1929317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 05/04/2021] [Accepted: 05/09/2021] [Indexed: 10/21/2022]
Abstract
We investigate the impact of IL-1A, IL-1B and IL-1R1 polymorphism on lymphoma. This study consisted of 155 Non-Hodgkin's lymphoma (NHL) patients 55 Hodgkin's lymphoma (HL) patients and 150 healthy individuals. PCR-RFLP method and ARMS PCR were used for genotyping of IL-1A rs3783553, IL-1B rs3917356, rs16944, IL-1R1 rs10490571 and IL-1A rs3783550 polymorphism. The results showed that the CC genotype of rs3783550 as well Ins/del of rs3783553 increased the risk of NHL. In contrast the AG genotype of rs3917356 and AG also AG + AA genotype of rs10490571 decreased the risk of NHL. The result revealed that the CC genotype of rs3783550 and AG genotype of rs3917356 increased risk of HL.
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Affiliation(s)
- Hosna Sarani
- Children and Adolescent Health Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
- Genetics of Non-communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Behrouz Mollashahi
- 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, Manitoba, Canada
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14
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Tracking the Genetic Susceptibility Background of B-Cell Non-Hodgkin's Lymphomas from Genome-Wide Association Studies. Int J Mol Sci 2020; 22:ijms22010122. [PMID: 33374413 PMCID: PMC7795678 DOI: 10.3390/ijms22010122] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/10/2020] [Accepted: 12/18/2020] [Indexed: 12/31/2022] Open
Abstract
B-cell non-Hodgkin’s lymphoma (NHL) risk associations had been mainly attributed to family history of the disease, inflammation, and immune components including human leukocyte antigen (HLA) genetic variations. Nevertheless, a broad range of genome-wide association studies (GWAS) have shed light into the identification of several genetic variants presumptively associated with B-cell NHL etiologies, survival or shared genetic risk with other diseases. The present review aims to overview HLA structure and diversity and summarize the evidence of genetic variations, by GWAS, on five NHL subtypes (diffuse large B-cell lymphoma DLBCL, follicular lymphoma FL, chronic lymphocytic leukemia CLL, marginal zone lymphoma MZL, and primary central nervous system lymphoma PCNSL). Evidence indicates that the HLA zygosity status in B-cell NHL might promote immune escape and that genome-wide significance variants can give biological insight but also potential therapeutic markers such as WEE1 in DLBCL. However, additional studies are needed, especially for non-DLBCL, to replicate the associations found to date.
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15
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Ivanova M, Shivarov V. HLA genotyping meets response to immune checkpoint inhibitors prediction: A story just started. Int J Immunogenet 2020; 48:193-200. [PMID: 33112034 DOI: 10.1111/iji.12517] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 10/06/2020] [Accepted: 10/13/2020] [Indexed: 12/27/2022]
Abstract
The implementation of the immune checkpoint blockade as a therapeutic option in contemporary oncology is one of the significant immunological achievements in the last century. Constantly accumulating evidence suggests that the response to immune checkpoint inhibitors (ICIs) is not universal. Therefore, it is critical to identify determinants for response, resistance and adverse effects of immune checkpoint therapy that could be developed as prognostic and predictive markers. Recent large scale analyses of cancer genome data revealed the key role of HLA class I and class II molecules in cancer immunoediting, and it appears that HLA diversity can predict response to ICIs. In the present review, we summarize the emerging data on the role of HLA germline variations as a marker for response to ICIs.
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Affiliation(s)
- Milena Ivanova
- Department of Clinical Immunology, University Hospital Alexandrovska, Medical University Sofia, Sofia, Bulgaria
| | - Velizar Shivarov
- Department of Genetics, St. Kliment Ohridski University, Sofia, Bulgaria
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16
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Iveland TS, Hagen L, Sharma A, Sousa MML, Sarno A, Wollen KL, Liabakk NB, Slupphaug G. HDACi mediate UNG2 depletion, dysregulated genomic uracil and altered expression of oncoproteins and tumor suppressors in B- and T-cell lines. J Transl Med 2020; 18:159. [PMID: 32264925 PMCID: PMC7137348 DOI: 10.1186/s12967-020-02318-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 03/27/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND HDAC inhibitors (HDACi) belong to a new group of chemotherapeutics that are increasingly used in the treatment of lymphocyte-derived malignancies, but their mechanisms of action remain poorly understood. Here we aimed to identify novel protein targets of HDACi in B- and T-lymphoma cell lines and to verify selected candidates across several mammalian cell lines. METHODS Jurkat T- and SUDHL5 B-lymphocytes were treated with the HDACi SAHA (vorinostat) prior to SILAC-based quantitative proteome analysis. Selected differentially expressed proteins were verified by targeted mass spectrometry, RT-PCR and western analysis in multiple mammalian cell lines. Genomic uracil was quantified by LC-MS/MS, cell cycle distribution analyzed by flow cytometry and class switch recombination monitored by FACS in murine CH12F3 cells. RESULTS SAHA treatment resulted in differential expression of 125 and 89 proteins in Jurkat and SUDHL5, respectively, of which 19 were commonly affected. Among these were several oncoproteins and tumor suppressors previously not reported to be affected by HDACi. Several key enzymes determining the cellular dUTP/dTTP ratio were downregulated and in both cell lines we found robust depletion of UNG2, the major glycosylase in genomic uracil sanitation. UNG2 depletion was accompanied by hyperacetylation and mediated by increased proteasomal degradation independent of cell cycle stage. UNG2 degradation appeared to be ubiquitous and was observed across several mammalian cell lines of different origin and with several HDACis. Loss of UNG2 was accompanied by 30-40% increase in genomic uracil in freely cycling HEK cells and reduced immunoglobulin class-switch recombination in murine CH12F3 cells. CONCLUSION We describe several oncoproteins and tumor suppressors previously not reported to be affected by HDACi in previous transcriptome analyses, underscoring the importance of proteome analysis to identify cellular effectors of HDACi treatment. The apparently ubiquitous depletion of UNG2 and PCLAF establishes DNA base excision repair and translesion synthesis as novel pathways affected by HDACi treatment. Dysregulated genomic uracil homeostasis may aid interpretation of HDACi effects in cancer cells and further advance studies on this class of inhibitors in the treatment of APOBEC-expressing tumors, autoimmune disease and HIV-1.
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Affiliation(s)
- Tobias S Iveland
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health, Norwegian University of Science and Technology, 7491, Trondheim, Norway.,Cancer Clinic, St. Olav's Hospital, Trondheim, Norway
| | - Lars Hagen
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health, Norwegian University of Science and Technology, 7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olav's Hospital, Trondheim, Norway.,Proteomics and Modomics Experimental Core, PROMEC, at NTNU and the Central Norway Regional Health Authority, Stjørdal, Norway
| | - Animesh Sharma
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health, Norwegian University of Science and Technology, 7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olav's Hospital, Trondheim, Norway.,Proteomics and Modomics Experimental Core, PROMEC, at NTNU and the Central Norway Regional Health Authority, Stjørdal, Norway
| | - Mirta M L Sousa
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health, Norwegian University of Science and Technology, 7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olav's Hospital, Trondheim, Norway
| | - Antonio Sarno
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health, Norwegian University of Science and Technology, 7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olav's Hospital, Trondheim, Norway
| | - Kristian Lied Wollen
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Nina Beate Liabakk
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health, Norwegian University of Science and Technology, 7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olav's Hospital, Trondheim, Norway
| | - Geir Slupphaug
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health, Norwegian University of Science and Technology, 7491, Trondheim, Norway. .,Clinic of Laboratory Medicine, St. Olav's Hospital, Trondheim, Norway. .,Proteomics and Modomics Experimental Core, PROMEC, at NTNU and the Central Norway Regional Health Authority, Stjørdal, Norway.
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