Immunologic features of nontuberculous mycobacterial pulmonary disease based on spatially resolved whole transcriptomics

• Published in: BMC pulmonary medicine 2024-08, Vol.24 (1), p.392-11, Article 392
• Main Authors: Koh, Jaemoon, Kim, Sehui, Kim, Joong-Yub, Yim, Jae-Joon, Kwak, Nakwon
• Format: Article
• Language: English
• Subjects: Adult; Aged; Analysis; Antigen presentation; Antigens; Bronchiectasis; Bronchiectasis - genetics; Bronchiectasis - immunology; Bronchiectasis - microbiology; CD28 antigen; CD3 antigen; CD40 antigen; CD80 antigen; Cell activation; Cells; DNA sequencing; Female; Foxp3 protein; Gene expression; Gene Expression Profiling; Gene set enrichment analysis; Genes; Humans; Immunohistochemistry; Infections; Lung - immunology; Lung - microbiology; Lung - pathology; Lung disease; Lung diseases; Lung Diseases - genetics; Lung Diseases - immunology; Lung Diseases - microbiology; Lymphocytes; Lymphocytes T; M1 phenotype; Macrophage activation; Macrophages; Macrophages - immunology; Macrophages - metabolism; Male; Middle Aged; Mycobacterium Infections, Nontuberculous - genetics; Mycobacterium Infections, Nontuberculous - immunology; Nontuberculous mycobacteria; Nontuberculous Mycobacteria - genetics; Nontuberculous Mycobacteria - immunology; Nucleotide sequencing; Phenotypes; RNA; RNA sequencing; Software; T cells; T-Lymphocytes - immunology; Transcriptome; Transcriptomes; Transcriptomics; Tuberculosis
• ISSN: 1471-2466; 1471-2466
• DOI: 10.1186/s12890-024-03207-2

The immunologic features of nontuberculous mycobacterial pulmonary disease (NTM-PD) are largely unclear. This study investigated the immunologic features of NTM-PD using digital spatial profiling techniques. Lung tissues obtained from six patients with NTM-PD between January 1, 2006, and December 31, 2020, at Seoul National University Hospital were subjected to RNA sequencing. Cores from the peribronchial areas were stained with CD3, CD68, and DNASyto13, and gene expression at the whole-transcriptome level was quantified using PCR amplification and Illumina sequencing. Lung tissues from six patients with bronchiectasis collected during the same period were used as controls. The RNA sequencing results were validated using immunohistochemistry (IHC) in another cohort (30 patients with NTM-PD and 15 patients with bronchiectasis). NTM-PD exhibited distinct gene expression patterns in T cells and macrophages. Gene set enrichment analysis revealed that pathways related to antigen presentation and processing were upregulated in NTM-PD, particularly in macrophages. Macrophages were more prevalent and the expression of genes associated with the M1 phenotype (CD40 and CD80) was significantly elevated. Although macrophages were activated in the NTM-PD group T cell activity was unaltered. Notably, expression of the costimulatory molecule CD28 was decreased in NTM-PD. IHC analysis showed that T cells expressing Foxp3 or TIM-3, which facilitate the regulatory functions of T cells, were increased. NTM-PD exhibits distinct immunologic signatures characterized by the activation of macrophages without T cell activation.