State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
Department of Electrical and Computer Engineering, The Grainger College of Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States.
Front Immunol. 2023 Mar 23;14:1103392. doi: 10.3389/fimmu.2023.1103392. eCollection 2023.
Systems characterization of immune landscapes in health, disease and clinical intervention cases is a priority in modern medicine. High-throughput transcriptomes accumulated from gene-knockout (KO) experiments are crucial for deciphering target KO signaling pathways that are impaired by KO genes at the systems-level. There is a demand for integrative platforms. This article describes the PathwayKO platform, which has integrated state-of-the-art methods of pathway enrichment analysis, statistics analysis, and visualizing analysis to conduct cutting-edge integrative pathway analysis in a pipeline fashion and decipher target KO signaling pathways at the systems-level. We focus on describing the methodology, principles and application features of PathwayKO. First, we demonstrate that the PathwayKO platform can be utilized to comprehensively analyze real-world mouse KO transcriptomes (GSE22873 and GSE24327), which reveal systemic mechanisms underlying the innate immune responses triggered by non-infectious extensive hepatectomy (2 hours after 85% liver resection surgery) and infectious CASP-model sepsis (12 hours after CASP-model surgery). Strikingly, our results indicate that both cases hit the same core set of 21 KO MyD88-associated signaling pathways, including the Toll-like receptor signaling pathway, the NFκB signaling pathway, the MAPK signaling pathway, and the PD-L1 expression and PD-1 checkpoint pathway in cancer, alongside the pathways of bacterial, viral and parasitic infections. These findings suggest common fundamental mechanisms between these immune responses and offer informative cues that warrant future experimental validation. Such mechanisms in mice may serve as models for humans and ultimately guide formulating the research paradigms and composite strategies to reduce the high mortality rates of patients in intensive care units who have undergone successful traumatic surgical treatments. Second, we demonstrate that the PathwayKO platform model-based assessments can effectively evaluate the performance difference of pathway analysis methods when benchmarked with a collection of proper transcriptomes. Together, such advances in methods for deciphering biological insights at the systems-level may benefit the fields of bioinformatics, systems immunology and beyond.
在现代医学中，对健康、疾病和临床干预病例中的免疫景观进行系统描述是当务之急。从基因敲除 (KO) 实验中积累的高通量转录组对于在系统水平上破译因 KO 基因而受损的目标 KO 信号通路至关重要。因此，人们需要整合平台。本文介绍了 PathwayKO 平台，该平台集成了先进的通路富集分析、统计分析和可视化分析方法，以流水线方式进行前沿的综合通路分析，并在系统水平上破译目标 KO 信号通路。我们重点介绍了 PathwayKO 的方法学、原理和应用特点。首先，我们证明了 PathwayKO 平台可用于全面分析真实的小鼠 KO 转录组 (GSE22873 和 GSE24327)，这些转录组揭示了非传染性广泛肝切除术后 (肝切除术后 2 小时) 和传染性 CASP 模型脓毒症 (CASP 模型手术后 12 小时) 引发的固有免疫反应的系统机制。令人惊讶的是，我们的结果表明，这两种情况都击中了相同的 21 个 KO MyD88 相关信号通路的核心集合，包括 Toll 样受体信号通路、NFκB 信号通路、MAPK 信号通路、以及 PD-L1 表达和癌症中的 PD-1 检查点通路，以及细菌、病毒和寄生虫感染的通路。这些发现表明这些免疫反应之间存在共同的基本机制，并提供了有价值的线索，值得进一步实验验证。这些在小鼠中的机制可能是人类的模型，并最终指导制定研究范式和综合策略，以降低成功接受创伤性手术治疗的重症监护病房患者的高死亡率。其次，我们证明了 PathwayKO 平台的模型评估可以有效地评估基于适当转录组的通路分析方法的性能差异。这些在系统水平上破译生物学见解的方法学进展可能有助于生物信息学、系统免疫学等领域的发展。
