دورية أكاديمية
Functional multigenic variations associated with hodgkin lymphoma.
العنوان: | Functional multigenic variations associated with hodgkin lymphoma. |
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المؤلفون: | Osman Y; Pathology Department, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia., Elsharkawy T; Pathology Department, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia., Hashim TM; Pathology Department, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia., Alratroot JA; Pathology Department, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia., Alsuwat HS; Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia., Otaibi WMA; Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia., Hegazi FM; Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia., AbdulAzeez S; Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia., Borgio JF; Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia. |
المصدر: | International journal of laboratory hematology [Int J Lab Hematol] 2021 Dec; Vol. 43 (6), pp. 1472-1482. Date of Electronic Publication: 2021 Jul 03. |
نوع المنشور: | Journal Article |
اللغة: | English |
بيانات الدورية: | Publisher: Blackwell Scientific Publications Country of Publication: England NLM ID: 101300213 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1751-553X (Electronic) Linking ISSN: 17515521 NLM ISO Abbreviation: Int J Lab Hematol Subsets: MEDLINE |
أسماء مطبوعة: | Original Publication: Oxford : Blackwell Scientific Publications, c2007- |
مواضيع طبية MeSH: | Genetic Association Studies*/methods , Genetic Heterogeneity* , Genetic Predisposition to Disease* , Genetic Variation*, Hodgkin Disease/*diagnosis , Hodgkin Disease/*etiology, Alleles ; Case-Control Studies ; Genotype ; Haplotypes ; Humans ; Phenotype ; Polymorphism, Single Nucleotide ; Saudi Arabia ; Exome Sequencing |
مستخلص: | Introduction: The current study aimed to describe genotypes associated with Hodgkin lymphoma (HL) in a cohort of Saudi and non-Saudi patients and discuss their possible susceptibility to HL. Methods: We studied clinical, histopathological, and laboratory findings of HL patients admitted over 12 years duration, at King Fahd University Hospital, KSA. The genomic DNAs of HL patients (n = 61) and normal control subjects (n = 36) were extracted, and genotyping was performed using the Illumina human exome bead chip. Set of HL patients and set of normal controls were included in this study. Results: A total of 35 DNA variants were found to be highly significant with the P-value <9.90 × 10 -11 among 243 345 exonic biomarkers and obeying the Hardy-Weinberg equilibrium. Nine, MEGF11-rs150945752 (P-value 1.20 × 10 -12 ), CACNA1I- s58055559 (P-value 1.93 × 10 -12 ), DECR2-rs146760080 (P-value 2.19 × 10 -12 ), STAB1-rs143894786 (P-value 2.45 × 10 -12 ), ZNF526-rs144433879 (P-value 2.76 × 10 -12 ), CPLANE1-rs200612080 (P-value 3.77 × 10 -12 ), DLK1-rs1058009 (P-value 5.95 × 10 -12 ), RTN4RL2-rs61745214 (P-value 7.71 × 10 -12 ), and PGRMC1-rs145582672 (P-value 8.56 × 10 -12 ), exonic variants on chromosomes 15, 22, and 16 were highly associated with HL cases. THE HIGHLY SIGNIFICANT HAPLOTYPES AT CHROMOSOME 3: rs143894786G; rs149982219G with P-value = 3.43 × 10 -14 was found to be the risk haplotype for the HL patients. The opposite alleles at chromosome 3: rs143894786A; rs149982219G is protective with P-value = 2.46 × 10 -12 . Maximum number of SNPs at the chromosome 19: rs144433879C; rs181265966G; rs201144421C; rs145591797G; rs200560875G; rs77270337G (risk P-value = 2.24 × 10 -12 ) and its opposite allele rs144433879A; rs181265966A; rs201144421T; rs145591797A; rs200560875A; rs77270337A (protective P-value = 2.60 × 10 -9 ) were found to be associated haplotype with the HL and controls, respectively, in Saudi population. Conclusion: Our study concludes that the HL is genetically heterogeneous with multigene causation. (© 2021 John Wiley & Sons Ltd.) |
References: | Kushekhar K, Van den Berg A, Nolte I, et al. Genetic associations in classical hodgkin lymphoma: a systematic review and insights into susceptibility mechanisms. Cancer Epidemiol Biomarkers Prev. 2014;23(12):2737-2747. Swerdlow SH, Campo E, Harris NL, et al., World Health Organization Classification of Tumours: Pathology and Genetics of Tumours of Haematopoietic and Lymphoid Tissues, 4th edn. Lyon, France: IARC Press; 2008. Swerdlow SH, Campo E, Pileri SA, et al. The 2016 revision of the World Health Organization classification of lymphoid neoplasms. Blood. 2016;127(20):2375-2390. Küppers R. The biology of Hodgkin's lymphoma. Nat Rev Cancer. 2009;9(1):15-27. Mathas S, Hartmann S, Küppers R. Hodgkin lymphoma: pathology and biology. Semin Hematol. 2016;53(3):139-147. Elgui de Oliveira D, Bacchi MM, Abreu ES, et al. Hodgkin disease in adult and juvenile groups from two different geographic regions in Brazil: characterization of clinicopathologic aspects and relationship with Epstein-Barr virus infection. Am J Clin Pathol. 2002;118:25-30. Araujo I, Bittencourt AL, Barbosa HS, et al. The high frequency of EBV infection in pediatric Hodgkin lymphoma is related to the classical type in Bahia, Brazil. Virchows Arch. 2006;449:315-319. Goldin LR, Pfeiffer RM, Gridley G, et al. Familial aggregation of Hodgkin lymphoma and related tumors. Cancer. 2004;100:1902-1908. Mack TM, Cozen W, Shibata DK, et al. Concordance for Hodgkin's disease in identical twins suggesting genetic susceptibility to the young-adult form of the disease. N Engl J Med. 1995;332:413-418. Shugart YY, Hemminki K, Vaittinen P, et al. A genetic study of Hodgkin's lymphoma: an estimate of heritability and anticipation based on the familial cancer database in Sweden. Hum Genet. 2000;106:553-556. Diepstra A, Niens M, te Meerman GJ, et al. Genetic susceptibility to Hodgkin's lymphoma associated with the human leukocyte antigen region. Eur J Haematol (Suppl). 2005;34-41. Goldin LR, McMaster ML, Ter-Minassian M, et al. A genome screen of families at high risk for Hodgkin lymphoma: evidence for a susceptibility gene on chromosome 4. J Med Genet. 2005;42:595-601. Liang XS, Caporaso N, Lou MM, et al. Common genetic variants in candidate genes and risk of familial lymphoid malignancies. Br J Haematol. 2009;146:418-423. Lawrie A, Cezard T, Culligan DJ, et al. Exome sequencing and linkage analysis implicates two candidate genes on chromosome 3p in familial hodgkin lymphoma. Blood. 2012;120(21):53. Cozen W, Timofeeva MN, Li D, et al. A meta-analysis of Hodgkin lymphoma reveals 19p13.3 TCF3 as a novel susceptibility locus. Nat Commun. 2014;5:3856. https://doi.org/10.1038/ncomms4856. Enciso-Mora V, Broderick P, Ma Y, et al. A genome-wide association study of Hodgkin’s lymphoma identifies new susceptibility loci at 2p16.1 (REL), 8q24.21 and 10p14 (GATA3). Nat Genet. 2010;42:1126-1130. https://doi.org/10.1038/ng.696. Frampton M, da Silva Filho MI, Broderick P, et al. Variation at 3p24.1 and 6q23.3 influences the risk of Hodgkin’s lymphoma. Nat Commun. 2013;4:2549. https://doi.org/10.1038/ncomms3549. Urayama KY, Jarrett RF, Hjalgrim H, et al. Genome-wide association study of classical Hodgkin lymphoma and Epstein-Barr virus status-defined subgroups. J Natl Cancer Inst. 2012;104(3):240-253. Thomsen H, da Silva Filho MI, Foersti A, et al. Heritability estimates on Hodgkin’s lymphoma: a genomic-versus population-based approach. Eur J Hum Genet. 2015;23(6):824-830. https://doi.org/10.1038/ejhg.2014.184. Sud A, Thomsen H, Law PJ, et al. Genome-wide association study of classical Hodgkin lymphoma identifies key regulators of disease susceptibility. Nat Commun. 2017;8:1892. https://doi.org/10.1038/s41467-017-00320-1. Glusman G, Caballero J, Mauldin DE, et al. An accessible system for testing SNV novelty. Bioinformatics. 2011;27:3216-3217. https://doi.org/10.1093/bioinformatics/btr540. Dayem Ullah AZ, Lemoine NR, Chelala C. SNPnexus: a web server for functional annotation of novel and publicly known genetic variants (2012 update). Nucleic Acids Res. 2012;40(W1):W65-W70. https://doi.org/10.1093/nar/gks364. Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2008;4:44-57. https://doi.org/10.1038/nprot.2008.211. Szklarczyk D, Morris JH, Cook H, et al. The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. Nucleic Acids Res. 2017;45(D1):D362-D368. https://doi.org/10.1093/nar/gkw937. Purcell S, Neale B, Todd-Brown K, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;8:559-575. Barrett JC, Fry B, Maller JDMJ, et al. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics. 2005;2:1263-1265. https://doi.org/10.1093/bioinformatics/bth457. Alsubaie LM, Alsuwat HS, Almandil NB, et al. Risk Y-haplotypes and pathogenic variants of Arab-ancestry boys with autism by an exome-wide association study. Mol Biol Rep. 2020;47(10):7623-7632. Al Asoom LI, Alsuwat HS, Rafique N, et al. Functional DNA variations associated with Saudi female with low VO2max: a pilot microarray study. Am J Transl Res. 2019;11(6):3659-3670. Zhao J, Cheng W, He X, et al. Construction of a specific SVM classifier and identification of molecular markers for lung adenocarcinoma based on lncRNA-miRNA-mRNA network. OncoTargets Ther. 2018;11:3129-3140. Kotani S, Yoda A, Kon A, et al. Molecular pathogenesis of disease progression in MLL-rearranged AML. Leukemia. 2019;33(3):612-624. Yang W, Ernst P. SET/MLL family proteins in hematopoiesis and leukemia. Int J Hematol. 2017;105(1):7-16. Tiziana Storlazzi C, Pieri L, Paoli C, et al. Complex karyotype in a polycythemia vera patient with a novel SETD1B/GTF2H3 fusion gene. Am J Hematol. 2014;89(4):438-442. Huang Y, Rao A. Connections between TET proteins and aberrant DNA modification in cancer. Trends Genet. 2014;30(10):464-474. Couronné L, Bastard C, Bernard OA. TET2 and DNMT3A mutations in human T-cell lymphoma. N Engl J Med. 2012;366(1):95-96. Manteniotis S, Wojcik S, Brauhoff P, et al. Functional characterization of the ectopically expressed olfactory receptor 2AT4 in human myelogenous leukemia. Cell Death Discovery. 2016;2:15070. https://doi.org/10.1038/cddiscovery.2015.70. Vosberg S, Hartmann L, Metzeler KH, et al. Relapse of acute myeloid leukemia after allogeneic stem cell transplantation is associated with gain of WT1 alterations and high mutation load. Haematologica. 2018;103(12):e581-e584. Shrestha R, Sakata-Yanagimoto M, Maie K, et al. Molecular pathogenesis of progression to myeloid leukemia from TET-insufficient status. Blood Adv. 2020;4(5):845-854. Aya-Bonilla C, Camilleri E, Haupt LM, et al. In silico analyses reveal common cellular pathways affected by loss of heterozygosity (LOH) events in the lymphomagenesis of Non-Hodgkin’s lymphoma (NHL). BMC Genom. 2014;15:390. Fernandez-Pol S, Costa HA, Steiner DF, et al. High-throughput sequencing of subcutaneous panniculitis-like T-cell lymphoma reveals candidate pathogenic mutations. Appl Immunohistochem Mol Morphol. 2019;27(10):740-748. Sala C, Arcangeli A. Reduced BCR signaling and a metabolic shift accompanies malignant progression of follicular lymphoma: a lesson from transcriptomics. Arch Cancer Biol Ther. 2020;1(2):31-36. Phan NN, Wang CY, Chen CF, et al. Voltage-gated calcium channels: novel targets for cancer therapy. Oncol Lett. 2017;14(2):2059-2074. Christodoulou CC, Zachariou M, Tomazou M, et al. Investigating the transition of pre-symptomatic to symptomatic huntington’s disease status based on omics data. Int J Mol Sci. 2020;21(19):7414. https://doi.org/10.3390/ijms21197414. Wang CY, Lai MD, Phan NN, et al. Meta-analysis of microarray datasets reveals voltage-gated calcium gene signatures in clinical cancer patients. PLoS One. 2015;10(7):e0125766. https://doi.org/10.1371/journal.pone.0125766. Tun HW, Personett D, Baskerville KA, et al. Pathway analysis of primary central nervous system lymphoma. Blood. 2008;111(6):3200-3210. Sørlie T, Wang Y, Xiao C, et al. Distinct molecular mechanisms underlying clinically relevant subtypes of breast cancer: gene expression analyses across three different platforms. BMC Genom. 2006;7:127. https://doi.org/10.1186/1471-2164-7-127. Al-Kuraya K, Narayanappa R, Al-Dayel F, et al. Epstein-Barr virus infection is not the sole cause of high prevalence for Hodgkin's lymphoma in Saudi Arabia. Leuk Lymphoma. 2006;47(4):707-713. |
معلومات مُعتمدة: | The Deanship of Scientific Research; 2017-135-IRMC Imam Abdulrahman Bin Faisal University |
فهرسة مساهمة: | Keywords: hodgkin lymphoma; microarray; multigenic variations |
تواريخ الأحداث: | Date Created: 20210703 Date Completed: 20211214 Latest Revision: 20221207 |
رمز التحديث: | 20221213 |
DOI: | 10.1111/ijlh.13644 |
PMID: | 34216518 |
قاعدة البيانات: | MEDLINE |
تدمد: | 1751-553X |
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DOI: | 10.1111/ijlh.13644 |