Table_5_Algorithm-Based Meta-Analysis Reveals the Mechanistic Interaction of the Tumor Suppressor LIMD1 With Non-Small-Cell Lung Carcinoma.xlsx

Non-small-cell lung carcinoma (NSCLC) is the major type of lung cancer, which is among the leading causes of cancer-related deaths worldwide. LIMD1 was previously identified as a tumor suppressor in lung cancer, but their detailed interaction in this setting remains unclear. In this study, we have carried out multiple genome-wide bioinformatic analyses for a comprehensive understanding of LIMD1 in NSCLC, using various online algorithm platforms that have been built for mega databases derived from both clinical and cell line samples. Our results indicate that LIMD1 expression level is significantly downregulated at both mRNA and protein levels in both lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), with a considerable contribution from its promoter methylation rather than its gene mutations. The Limd1 gene undergoes mutation only at a low rate in NSCLC (0.712%). We have further identified LIMD1-associated molecular signatures in NSCLC, including its natural antisense long non-coding RNA LIMD1-AS1 and a pool of membrane trafficking regulators. We have also identified a subgroup of tumor-infiltrating lymphocytes, especially neutrophils, whose tumor infiltration levels significantly correlate with LIMD1 level in both LUAD and LUSC. However, a significant correlation of LIMD1 with a subset of immune regulatory molecules, such as IL6R and TAP1, was only found in LUAD. Regarding the clinical outcomes, LIMD1 expression level only significantly correlates with the survival of LUAD (p<0.01) but not with that of LUSC (p>0.1) patients. These findings indicate that LIMD1 plays a survival role in LUAD patients at least by acting as an immune regulatory protein. To further understand the mechanisms underlying the tumor-suppressing function of LIMD1 in NSCLC, we show that LIMD1 downregulation remarkably correlates with the deregulation of multiple pathways that play decisive roles in the oncogenesis of NSCLC, especially those mediated by EGFR, KRAS, PIK3CA, Keap1, and p63, in both LUAD and LUSC, and those mediated by p53 and CDKN2A only in LUAD. This study has disclosed that LIMD1 can serve as a survival prognostic marker for LUAD patients and provides mechanistic insights into the interaction of LIMD1 with NSCLC, which provide valuable information for clinical applications.

非小细胞肺癌（Non-small-cell lung carcinoma, NSCLC）是肺癌的主要亚型，亦是全球范围内癌症相关死亡的首要诱因之一。LIMD1此前已被鉴定为肺癌中的肿瘤抑制因子，但二者在该疾病背景下的具体相互作用仍未明确。本研究依托针对临床样本与细胞系样本构建的大型数据库所开发的各类在线算法平台，开展了多项全基因组生物信息学分析，以全面解析LIMD1在非小细胞肺癌中的作用。研究结果显示，在肺腺癌（lung adenocarcinoma, LUAD）与肺鳞状细胞癌（lung squamous cell carcinoma, LUSC）中，LIMD1的mRNA（messenger RNA）与蛋白质表达水平均显著下调，其下调主要源于启动子甲基化，而非基因突变。LIMD1基因在非小细胞肺癌中的突变率仅为0.712%，处于较低水平。本研究进一步鉴定了非小细胞肺癌中与LIMD1相关的分子特征，包括其天然反义长链非编码RNA LIMD1-AS1，以及一组膜运输调控因子。同时，我们还发现了一类肿瘤浸润淋巴细胞亚群（尤以中性粒细胞为代表），其肿瘤浸润水平在肺腺癌与肺鳞状细胞癌中均与LIMD1表达水平显著相关。不过，LIMD1与部分免疫调控分子（如IL6R、TAP1）的显著相关性仅见于肺腺癌患者中。关于临床结局，LIMD1的表达水平仅与肺腺癌患者的生存情况显著相关（p<0.01），而与肺鳞状细胞癌患者的生存无显著关联（p>0.1）。上述结果表明，LIMD1至少可通过作为免疫调控蛋白的方式，对肺腺癌患者发挥生存保护作用。为进一步阐明LIMD1在非小细胞肺癌中发挥肿瘤抑制功能的潜在机制，本研究证实：在肺腺癌与肺鳞状细胞癌中，LIMD1的下调均与多条在非小细胞肺癌发生发展中起决定性作用的信号通路失调显著相关，尤其是由EGFR、KRAS、PIK3CA、Keap1及p63介导的通路；而由p53与CDKN2A介导的通路失调仅与肺腺癌中的LIMD1下调相关。本研究揭示，LIMD1可作为肺腺癌患者的生存预后标志物，并为解析LIMD1与非小细胞肺癌的相互作用提供了机制层面的见解，可为临床应用提供有价值的参考信息。