Gene biomarkers and classifiers for various subtypes of HTLV-1-caused ATLL cancer identified by a combination of differential gene co‑expression and support vector machine algorithms.

IF 5.5 3区医学 Q1 IMMUNOLOGY

Medical Microbiology and Immunology Pub Date : 2023-08-01 DOI:10.1007/s00430-023-00767-8

Mohadeseh Zarei Ghobadi, Elaheh Afsaneh, Rahman Emamzadeh

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Abstract

Adult T-cell leukemia/lymphoma (ATLL) is pathogen-caused cancer that is progressed after the infection by human T-cell leukemia virus type 1. Four significant subtypes comprising acute, lymphoma, chronic, and smoldering have been identified for this cancer. However, there are no trustworthy prognostic biomarkers for these subtypes. We utilized a combination of two powerful network-based and machine-learning algorithms including differential co-expressed genes (DiffCoEx) and support vector machine-recursive feature elimination with cross-validation (SVM-RFECV) methods to categorize disparate ATLL subtypes from asymptomatic carriers (ACs). The results disclosed the significant involvement of CBX6, CNKSR1, and MAX in chronic, MYH10 and P2RY1 in acute, C22orf46 and HNRNPA0 in smoldering subtypes. These genes also can classify each ATLL subtype from AC carriers. The integration of the results of two powerful algorithms led to the identification of reliable gene classifiers and biomarkers for diverse ATLL subtypes.

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通过差异基因共表达和支持向量机算法的组合鉴定htlv -1引起的ATLL癌症的各种亚型的基因生物标志物和分类器。

成人t细胞白血病/淋巴瘤(Adult T-cell leukemia/lymphoma, ATLL)是一种由病原体引起的癌症，在感染1型人t细胞白血病病毒后发生进展。四种重要的亚型包括急性，淋巴瘤，慢性和阴燃已确定为这种癌症。然而，对于这些亚型，还没有可靠的预后生物标志物。我们结合了两种强大的基于网络和机器学习的算法，包括差分共表达基因(DiffCoEx)和支持向量机递归特征消除交叉验证(SVM-RFECV)方法，对无症状携带者(ACs)的不同ATLL亚型进行分类。结果显示CBX6、CNKSR1和MAX在慢性中显著参与，MYH10和P2RY1在急性中显著参与，C22orf46和HNRNPA0在阴燃亚型中显著参与。这些基因也可以从AC携带者中区分ATLL亚型。两种强大算法的结果整合导致了对不同ATLL亚型的可靠基因分类器和生物标记物的鉴定。

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来源期刊

Medical Microbiology and Immunology 医学-免疫学

CiteScore

10.60

自引率

0.00%

发文量

审稿时长

1 months

期刊介绍： Medical Microbiology and Immunology (MMIM) publishes key findings on all aspects of the interrelationship between infectious agents and the immune system of their hosts. The journal´s main focus is original research work on intrinsic, innate or adaptive immune responses to viral, bacterial, fungal and parasitic (protozoan and helminthic) infections and on the virulence of the respective infectious pathogens. MMIM covers basic, translational as well as clinical research in infectious diseases and infectious disease immunology. Basic research using cell cultures, organoid, and animal models are welcome, provided that the models have a clinical correlate and address a relevant medical question. The journal also considers manuscripts on the epidemiology of infectious diseases, including the emergence and epidemic spreading of pathogens and the development of resistance to anti-infective therapies, and on novel vaccines and other innovative measurements of prevention. The following categories of manuscripts will not be considered for publication in MMIM: submissions of preliminary work, of merely descriptive data sets without investigation of mechanisms or of limited global interest, manuscripts on existing or novel anti-infective compounds, which focus on pharmaceutical or pharmacological aspects of the drugs, manuscripts on existing or modified vaccines, unless they report on experimental or clinical efficacy studies or provide new immunological information on their mode of action, manuscripts on the diagnostics of infectious diseases, unless they offer a novel concept to solve a pending diagnostic problem, case reports or case series, unless they are embedded in a study that focuses on the anti-infectious immune response and/or on the virulence of a pathogen.