College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China.
Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China.
Nat Commun. 2020 Feb 21;11(1):1000. doi: 10.1038/s41467-020-14802-2.
Long noncoding RNAs (lncRNAs) are emerging as critical regulators of gene expression and they play fundamental roles in immune regulation. Here we introduce an integrated algorithm, ImmLnc, for identifying lncRNA regulators of immune-related pathways. We comprehensively chart the landscape of lncRNA regulation in the immunome across 33 cancer types and show that cancers with similar tissue origin are likely to share lncRNA immune regulators. Moreover, the immune-related lncRNAs are likely to show expression perturbation in cancer and are significantly correlated with immune cell infiltration. ImmLnc can help prioritize cancer-related lncRNAs and further identify three molecular subtypes (proliferative, intermediate, and immunological) of non-small cell lung cancer. These subtypes are characterized by differences in mutation burden, immune cell infiltration, expression of immunomodulatory genes, response to chemotherapy, and prognosis. In summary, the ImmLnc pipeline and the resulting data serve as a valuable resource for understanding lncRNA function and to advance identification of immunotherapy targets.
长链非编码 RNA（lncRNAs）正在成为基因表达的关键调控因子，它们在免疫调节中发挥着重要作用。在这里，我们引入了一种综合算法 ImmLnc，用于鉴定免疫相关途径的 lncRNA 调控因子。我们全面描绘了 33 种癌症类型中免疫组中 lncRNA 调控的全景图，并表明具有相似组织起源的癌症可能具有相似的 lncRNA 免疫调控因子。此外，与免疫相关的 lncRNAs 可能在癌症中表现出表达失调，并与免疫细胞浸润显著相关。ImmLnc 可以帮助优先考虑与癌症相关的 lncRNAs，并进一步鉴定非小细胞肺癌的三种分子亚型（增殖型、中间型和免疫型）。这些亚型的特征是突变负担、免疫细胞浸润、免疫调节基因表达、对化疗的反应和预后存在差异。总之，ImmLnc 管道及其产生的数据为理解 lncRNA 功能和推进免疫治疗靶点的鉴定提供了有价值的资源。
