台灣人口中非結核分枝桿菌肺病的全基因組關聯分析

Genome-wide association study of non-tuberculous mycobacterial lung disease in Taiwanese population

陳姿吟(Tzu-Yin Chen)

指導教授 ： 顏伯勳

國立臺灣大學/醫學院/生物化學暨分子生物學研究所/碩士(2022年)

https://doi.org/10.6342/NTU202203920

摘要

分枝桿菌在臨床上可分為三大類，分別是結核分枝桿菌、麻風分枝桿菌和非結核分枝桿菌 (NTM)。NTM是環境中普遍存在的微生物，尤其生長在水和土壤中。有些NTM，像鳥型分枝桿菌復合體 (MAC) 和膿腫分枝桿菌屬於伺機性病菌，可能會引起肺部疾病 (NTM-LD)。由於NTM和結核分枝桿菌具有相似的性質，過去經常被誤診為結核病。近年全球NTM-LD的發病率和患病率逐漸增加。此外，NTM對抗生素有極強的抗藥性且NTM-LD難以治療。因此，對NTM感染增加原因的研究開始備受重視。NTM-LD通常不會在人與人之間傳播，但患有潛在肺病、免疫系統低下以及停經後瘦弱的女性有較高的風險感染NTM。先前的研究也證實NTM-LD患者存在遺傳易感性。然而，目前仍不清楚與NTM-LD易感性相關的遺傳因素。本論文主要是透過比對NTM-LD患者和健康人的基因體序列來尋找特定基因上的單核苷酸多態性 (single nucleotide polymorphism, SNP) 作為生物標記，並進一步探討遺傳變異與 NTM 易感性之間的關聯，從而提升NTM-LD的初步診斷與預防。我們透過全基因組關聯分析 (GWAS) 在兩組基因體序列之間發現有20個顯著差異的SNPs坐落於KIAA0825基因中。KIAA0825的已知主要產物有長、短兩個異構體，但功能仍未知。我們發現在病患檢體中長異構體的比例比健康控制組多，此外我們建立了CRISPR/Cas9的基因剔除系統並運用在巨噬細胞中，我們觀察到當THP1細胞株的KIAA0825基因剔除或是突變後，受刺激細胞的生長速度會受到影響，透過實驗我們發現KIAA0825基因可能扮演重要的角色來影響台灣人對NTM的遺傳易感性。儘管 KIAA0825 基因產物的功能尚不清楚，但經由分析主要長短兩種亞型 mRNA 的表現量，發現 KIAA0825 在 MAC-LD 患者中的長亞型比例較高。此外，也藉由 CRISPR/Cas9 基因組編輯系統建構了具有長亞型KIAA0825-基因剔除及全KIAA0825-基因剔除的 THP1 單核球細胞株。我們進一步證明，具有長亞型 KIAA0825-基因剔除或全 KIAA0825-基因剔除的 THP1 細胞生長速率會受到影響。這表明 KIAA0825 基因可能在巨噬細胞中發揮重要作用，使細胞在發炎和感染期間能維持其活力。

關鍵字

非結合分枝桿菌 ； 遺傳易感性 ； 單核苷酸多態性 ； 全基因組關聯分析 ； KIAA0825 ； CRISPR/Cas9剔除系統

並列摘要

Mycobacteria are a family of rod-shaped bacilli that are clinically classified into three major groups, including Mycobacterium tuberculosis, Mycobacterium leprae and Nontuberculous mycobacteria (NTM). NTM are ubiquitous in the environment and especially exist in water source and soil. Some NTM species, like Mycobacterium avium complex (MAC) and Mycobacterium abscessus, are pathogenic and would cause clinical diseases. NTM-lung disease (LD), the most common disease resulted from NTM infection, was often misdiagnosed as tuberculosis in the past due to the similar properties between NTM and M. tuberculosis. Recently, the incidence and prevalence of NTM-LD is increasing globally. Besides, NTM are extremely antibiotic resistant, and the disease is difficult to treat. Therefore, the reasons for the NTM increase are being elucidated in recent years. NTM-LD is typically not transmitted person-to-person, but people with underlying lung disease or depressed immune systems and thin women after menopause have a higher risk of NTM infection. The previous studies indicated that there are genetic predispositions in NTM-LD patients; however, genetic factors related to the NTM-LD susceptibility are still unclear. This study aims to identify specific single nucleotide polymorphisms (SNPs) on specific genes as biomarkers by comparing the gene sequences of NTM-LD patients and healthy people, and further to clarify the association between genetic variants and NTM susceptibility that could improve preliminary diagnosis and prevention for NTM-LD. Based on a genome-wide association study (GWAS) analysis, 20 SNPs on the KIAA0825 gene with significant differences between two groups have been identified. Although the function of KIAA0825 gene-encoded products is still unclear, we analyzed the mRNA expression of the major long and short isoforms and demonstrated that the long isoform proportion of KIAA0825 in MAC-LD patients was higher. In addition, THP1 monocytic leukemia cell lines with the long isoform KIAA0825-knockout or full KIAA0825-knockout have been established via a CRISPR/Cas9 genome editing system. We further demonstrated that the growth rate of the stimulated THP1 cell clones with the long isoform KIAA0825-knockout or full KIAA0825-knockout was affected. It suggests that the KIAA0825 gene may play an important role in macrophages to maintain their viability during inflammation and infection.

並列關鍵字

Nontuberculous mycobacteria (NTM) ； Genetic predisposition ； Single nucleotide polymorphisms (SNPs) ； Genome-wide association study (GWAS) ； KIAA0825 ； CRISPR/Cas9 knockout

參考文獻

1 Runyon, E. H. Anonymous mycobacteria in pulmonary disease. Med Clin North Am 43, 273-290, doi:10.1016/s0025-7125(16)34193-1 (1959).

2 Ding, L. W., Lai, C. C., Lee, L. N. et al. Disease caused by non-tuberculous mycobacteria in a university hospital in Taiwan, 1997-2003. Epidemiol Infect 134, 1060-1067, doi:10.1017/s0950268805005698 (2006).

3 Griffith, D. E., Aksamit, T., Brown-Elliott, B. A. et al. An official ATS/IDSA statement: diagnosis, treatment, and prevention of nontuberculous mycobacterial diseases. Am J Respir Crit Care Med 175, 367-416, doi:10.1164/rccm.200604-571ST (2007).

4 Falkinham, J. O., 3rd. Nontuberculous mycobacteria from household plumbing of patients with nontuberculous mycobacteria disease. Emerg Infect Dis 17, 419-424, doi:10.3201/eid1703.101510 (2011).

5 Honda, J. R., Virdi, R. Chan, E. D. Global Environmental Nontuberculous Mycobacteria and Their Contemporaneous Man-Made and Natural Niches. Front Microbiol 9, 2029, doi:10.3389/fmicb.2018.02029 (2018).