Table_3_Integrated Whole-Transcriptome Profiling and Bioinformatics Analysis of the Polypharmacological Effects of Ganoderic Acid Me in Colorectal Cancer Treatment.xlsx

Ganoderic acid Me (GA-Me) is a natural bioactive compound derived from Ganoderma lucidum. Our present results suggested that GA-Me inhibited proliferation, induced DNA fragmentation and significantly activated caspase-9 and caspase-3 in HCT116 cells. As shown in our previous studies, GA-Me targets several genes to prevent cancer, including colorectal cancer (CRC). Thus, we hypothesized that GA-Me might be a multitarget ligand against cancer. However, its exact mechanism in CRC remains unclear. Here, whole-transcriptome sequencing was employed to assess the long noncoding RNA (lncRNA), circular RNA (circRNA), microRNA (miRNA), and messenger RNA (mRNA) profiles of GA-Me-treated HCT116 cells. In total, 1572 differentially expressed (DE) lncRNAs, 123 DEcircRNAs, 87 DEmiRNAs, and 1508 DEmRNAs were identified. DCBLD2 and RAPGEF5 were validated as two core mRNAs in the DElncRNA, DEcircRNA, and DEmiRNA networks. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed the biological functions and potential mechanisms of TCONS-00008997, XR-925056.2, circRNA-07908, hsa-miR-100-3p, hsa-miR-1257, hsa-miR-3182, NAV3, ADAM20, and STARD4, which were altered after GA-Me treatment. The regulatory relationships of the XR-925056.2-hsa-miR-3182-NAV3/ADAM20/STARD4, circRNA-07908|Chr22:38986298-39025349-hsa-miR-3182-NAV3/ADAM20, ENST00000414039/ENST00000419190-novel874_mature-MMP9 and circRNA-00314|Chr1:35470863-35479212/circRNA-05460|Chr17:72592203-72649268-novel874_mature-MMP9 immune-regulatory networks involved both noncoding RNAs (ncRNAs) and mRNAs. Molecular docking studies showed that Zn2+ and the His201, His205, His211, Glu202, and Ala165 residues of MMP2 contributed to its high affinity for GA-Me. Zn2+ and the Glu402 and Gly186 residues of MMP9 are important for its interaction with GA-Me. Our results suggested and confirmed that GA-Me is a potential multitarget lead compound for CRC treatment with unique polypharmacological advantages.

赤芝酸Me（GA-Me）是一种源自灵芝（Ganoderma lucidum）的天然生物活性化合物。本研究结果提示，GA-Me能够抑制HCT116细胞的增殖，诱导DNA片段化，并显著激活caspase-9和caspase-3。如前述研究所示，GA-Me针对多种基因以预防癌症，包括结直肠癌（CRC）。因此，我们提出假设，GA-Me可能是一种针对癌症的多靶点配体。然而，其在CRC中的确切机制尚不明确。在本研究中，我们采用全转录组测序技术，评估了GA-Me处理后的HCT116细胞中的长非编码RNA（lncRNA）、环状RNA（circRNA）、微RNA（miRNA）和信使RNA（mRNA）的表达谱。共鉴定出1572个差异表达（DE）lncRNA、123个DEcircRNA、87个DEmiRNA和1508个DEmRNA。DCBLD2和RAPGEF5被验证为DElncRNA、DEcircRNA和DEmiRNA网络中的两个核心mRNA。基因本体（GO）和京都基因与基因组百科全书（KEGG）分析揭示了TCONS-00008997、XR-925056.2、circRNA-07908、hsa-miR-100-3p、hsa-miR-1257、hsa-miR-3182、NAV3、ADAM20和STARD4等在GA-Me处理后改变的生物功能和潜在机制。XR-925056.2-hsa-miR-3182-NAV3/ADAM20/STARD4、circRNA-07908|Chr22:38986298-39025349-hsa-miR-3182-NAV3/ADAM20、ENST00000414039/ENST00000419190-novel874_mature-MMP9和circRNA-00314|Chr1:35470863-35479212/circRNA-05460|Chr17:72592203-72649268-novel874_mature-MMP9等免疫调节网络涉及非编码RNA（ncRNA）和mRNA之间的调控关系。分子对接研究表明，Zn2+以及MMP2的His201、His205、His211、Glu202和Ala165残基对其与GA-Me的高亲和力有贡献。Zn2+以及MMP9的Glu402和Gly186残基对其与GA-Me的相互作用至关重要。我们的研究结果提示并证实，GA-Me是CRC治疗中具有独特多药理优势的潜在多靶点先导化合物。