Profiling the immune response to <i>Mycobacterium tuberculosis</i> Beijing family infection: a perspective from the transcriptome

Tuberculosis continues to be an important public health problem. Particularly considering Beijing-family strains of <i>Mycobacterium tuberculosis</i>, which have been associated with drug-resistance and hypervirulence. The Beijing-like SIT190 (BL) is the most prevalent Beijing strain in Colombia. The pathogenic mechanism and immune response against this pathogen is unknown. Thus, we compared the course of pulmonary TB in BALB/c mice infected with Classical-Beijing strain 391 and BL strain 323. The disease course was different among infected animals with Classical-Beijing and BL strain. Mice infected with BL had a 100% mortality at 45 days post-infection (dpi), with high bacillary loads and massive pneumonia, whereas infected animals with Classical-Beijing survived until 60 dpi and showed extensive pneumonia and necrosis. Lung RNA extraction was carried out at early (day 3 dpi), intermediate (day 14 dpi), and late (days 28 and 60 dpi) time points of infection. Transcriptional analysis of infected mice with Classical-Beijing showed several over-expressed genes, associated with a pro-inflammatory profile, including those for coding for CCL3 and CCL4 chemokines, both biomarkers of disease severity. Conversely, mice infected with BL displayed a profile which included the over-expression of several genes associated with immune-suppression, including <i>Nkiras, Dleu2,</i> and <i>Sphk2</i>, highlighting an anti-inflammatory milieu which would allow high bacterial replication followed by an intense inflammatory response. In summary, both Beijing strains induced a non-protective immune response which induced extensive tissue damage, BL strain induced rapidly extensive pneumonia and death, whereas Classical-Beijing strain produced slower extensive pneumonia later associated with extensive necrosis. <b>Abbreviations</b> <b>Mtb</b>: <i>Mycobacterium tuberculosis</i>; <b>SIT</b>: Spoligotype International Type; <b>TB</b>: Tuberculosis; <b>CTB</b>: Classical-typical Beijing; <b>BL</b>: Beijing-Like; <b>CCL3</b>: Chemokine (C-C motif) ligand 3 (CCL3); <b>CCL4</b>: Chemokine (C-C motif) ligand four (CCL4); <b>WHO</b>: World health Organization; <b>DR</b>: Direct Repeats; <b>IFN-γ</b>: Interferon Gamma; <b>IL</b>: Interleukin; <b>TGF-β</b>: Transforming Growth Factor Beta; <b>XDR</b>: Extremely Drug Resistant; <b>MDR</b>: Multi Drug Resistant; <b>MIRU-VNTR</b>: Mycobacterial Interspersed Repetitive Units–Variable Number Tandem repeats; <b>OADC</b>: Oleic Albumin Dextrose Catalase; <b>ATCC</b>: American Type Culture Collection; <b>MOI</b>: Multiplicity of Infection; <b>CFUs</b>: Colony Forming Units; <b>ELISA</b>: enzyme-linked immunosorbent assay; <b>qRT-PCR</b>: Real-Time Quantitative Reverse Transcription PCR; <b>RNA-seq</b>: Ribonucleic Acid sequencing; <b>RIN</b>: RNA Integrity Number; <b>RNA</b>: Ribonucleic Acid; <b>DNA</b>: Deoxyribonucleic Acid; <b>dsDNA HS</b>: Double stranded Deoxyribonucleic Acid High Sensitivity; <b>RAI</b>: Red de Apoyo à la Investigacion, Mexico City, Mexico; <b>DEG</b>: Differential Expressed Genes; <b>GO</b>: Gene Ontology; <b>KEGG</b>: Kyoto Encyclopedia of Genes and Genomes; <b>ORA</b>: Over-Representation Analysis; <b>SNPs</b>: Single Nucleotide Polymorphisms; <b>TNFα</b>: Tumoral necrosis factor alpha; <b>DE</b>: Differential Expression; <b>EPA</b>: Enrichment Pathways Analysis; <b>TLR</b>: Toll-Like receptor; <b>NLRP</b>: NOD-like receptor with Pyrin domain; <b>tRNA</b>: Transfer RNA; <b>MAPK</b>: Mitogen-Activated Protein Kinase; <b>NK</b>: Natural killer; <b>ATP</b>: Adenosine Triphosphate; <b>DGC</b>: dystrophin-glycoprotein complex; <b>PDIM</b>: Ptiocerol Dimicocerosate; <b>NCBI</b>: National Center for Bioinformatics Information

结核病仍是亟待防控的重要公共卫生问题，其中结核分枝杆菌（Mycobacterium tuberculosis）北京家族菌株尤为值得关注，该类菌株与耐药性及高毒力表型密切相关。北京样SIT190（BL）是哥伦比亚地区流行率最高的北京家族菌株，目前针对该病原菌的致病机制与宿主免疫应答仍未阐明。为此，本研究对比了感染经典北京株391与BL株323的BALB/c小鼠的肺结核病程。

感染两类菌株的小鼠肺结核病程存在显著差异：感染BL株的小鼠在感染后45天（dpi）全部死亡，同时伴随高细菌载量与重度肺炎；而感染经典北京株的小鼠可存活至感染后60天，表现为广泛性肺炎与组织坏死。

研究分别在感染早期（感染后第3天）、中期（感染后第14天）及晚期（感染后第28、60天）收取肺部组织进行RNA提取。对感染经典北京株的小鼠开展转录组分析发现，多个基因呈现过表达特征，与促炎表型相关，包括编码趋化因子CCL3与CCL4的基因，二者均为疾病严重程度的生物标志物。与之相反，感染BL株的小鼠则呈现免疫抑制相关的多个基因过表达表型，包括*Nkiras*、*Dleu2*与*Sphk2*，提示存在抗炎微环境，该环境可允许细菌大量复制，随后引发剧烈炎症反应。

综上，两类北京家族菌株均诱导了非保护性免疫应答，进而引发广泛组织损伤；BL株可快速诱导广泛性肺炎并导致宿主死亡，而经典北京株则引发进展较为缓慢的广泛性肺炎，后续伴随广泛组织坏死。

**缩写说明**
**Mtb**：结核分枝杆菌（Mycobacterium tuberculosis）；**SIT**：间隔区寡核苷酸分型国际型（Spoligotype International Type）；**TB**：结核病（Tuberculosis）；**CTB**：经典典型北京株（Classical-typical Beijing）；**BL**：北京样株（Beijing-Like）；**CCL3**：趋化因子（C-C基序）配体3（Chemokine (C-C motif) ligand 3, CCL3）；**CCL4**：趋化因子（C-C基序）配体4（Chemokine (C-C motif) ligand 4, CCL4）；**WHO**：世界卫生组织（World Health Organization）；**DR**：直接重复序列（Direct Repeats）；**IFN-γ**：γ干扰素（Interferon Gamma）；**IL**：白细胞介素（Interleukin）；**TGF-β**：转化生长因子β（Transforming Growth Factor Beta）；**XDR**：广泛耐药（Extremely Drug Resistant）；**MDR**：多药耐药（Multi Drug Resistant）；**MIRU-VNTR**：分枝杆菌散在重复单位-可变数目串联重复序列（Mycobacterial Interspersed Repetitive Units–Variable Number Tandem repeats）；**OADC**：油酸白蛋白葡萄糖过氧化氢酶培养基（Oleic Albumin Dextrose Catalase）；**ATCC**：美国模式培养物集存库（American Type Culture Collection）；**MOI**：感染复数（Multiplicity of Infection）；**CFUs**：菌落形成单位（Colony Forming Units）；**ELISA**：酶联免疫吸附试验（enzyme-linked immunosorbent assay）；**qRT-PCR**：实时定量反转录聚合酶链式反应（Real-Time Quantitative Reverse Transcription PCR）；**RNA-seq**：核糖核酸测序（Ribonucleic Acid sequencing）；**RIN**：RNA完整性数（RNA Integrity Number）；**RNA**：核糖核酸（Ribonucleic Acid）；**DNA**：脱氧核糖核酸（Deoxyribonucleic Acid）；**dsDNA HS**：高灵敏度双链脱氧核糖核酸（Double stranded Deoxyribonucleic Acid High Sensitivity）；**RAI**：墨西哥城研究支持网络（Red de Apoyo à la Investigacion, Mexico City, Mexico）；**DEG**：差异表达基因（Differential Expressed Genes）；**GO**：基因本体论（Gene Ontology）；**KEGG**：京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes）；**ORA**：富集分析（Over-Representation Analysis）；**SNPs**：单核苷酸多态性（Single Nucleotide Polymorphisms）；**TNFα**：肿瘤坏死因子α（Tumoral necrosis factor alpha）；**DE**：差异表达（Differential Expression）；**EPA**：通路富集分析（Enrichment Pathways Analysis）；**TLR**：Toll样受体（Toll-Like receptor）；**NLRP**：含pyrin结构域的NOD样受体（NOD-like receptor with Pyrin domain）；**tRNA**：转运RNA（Transfer RNA）；**MAPK**：丝裂原活化蛋白激酶（Mitogen-Activated Protein Kinase）；**NK**：自然杀伤（Natural killer）；**ATP**：三磷酸腺苷（Adenosine Triphosphate）；**DGC**：肌营养不良蛋白-糖蛋白复合物（dystrophin-glycoprotein complex）；**PDIM**：酚糖脂二分枝菌酸酯（Ptiocerol Dimicocerosate）；**NCBI**：美国国家生物技术信息中心（National Center for Bioinformatics Information）

搜集汇总

背景与挑战

背景概述

该数据集通过转录组分析，研究了小鼠感染结核分枝杆菌北京家族菌株（包括Classical-Beijing和BL菌株）的免疫反应。研究发现，两种菌株诱导非保护性免疫反应并导致广泛组织损伤，其中BL菌株引发快速广泛肺炎和死亡，而Classical-Beijing菌株导致较慢的广泛肺炎和坏死。数据集提供了早期、中期和晚期感染时间点的基因表达数据，用于揭示不同菌株的致病机制和免疫调控差异。