Molecular stratification using gene-level transcriptional data has identified subtypes with distinctive genotypic and phenotypic traits, as exemplified by the consensus molecular subtypes (CMS) in colorectal cancer (CRC). Here, rather than gene-level data, we make use of gene ontology and biological activation state information for initial molecular class discovery. In doing so, we defined three pathway-derived subtypes (PDS) in CRC: PDS1 tumors, which are canonical/LGR5⁺ stem-rich, highly proliferative and display good prognosis; PDS2 tumors, which are regenerative/ANXA1⁺ stem-rich, with elevated stromal and immune tumor microenvironmental lineages; and PDS3 tumors, which represent a previously overlooked slow-cycling subset of tumors within CMS2 with reduced stem populations and increased differentiated lineages, particularly enterocytes and enteroendocrine cells, yet display the worst prognosis in locally advanced disease. These PDS3 phenotypic traits are evident across numerous bulk and single-cell datasets, and demark a series of subtle biological states that are currently under-represented in pre-clinical models and are not identified using existing subtyping classifiers.

使用基因水平转录数据的分子分层已经确定了具有独特基因型和表型特征的亚型，结直肠癌 (CRC) 中的共有分子亚型 (CMS) 就是例证。在这里，我们利用基因本体和生物激活状态信息来进行初始分子类别发现，而不是基因级数据。在此过程中，我们定义了 CRC 中的三种途径衍生亚型 (PDS)： PDS1 肿瘤，富含典型/LGR5 ⁺干细胞，高度增殖且预后良好； PDS2 肿瘤，具有再生性/富含 ANXA1 ⁺干细胞，具有升高的基质和免疫肿瘤微环境谱系； PDS3 肿瘤代表了 CMS2 内先前被忽视的慢周期肿瘤子集，其干细胞群减少，分化谱系增加，特别是肠上皮细胞和肠内分泌细胞，但在局部晚期疾病中表现出最差的预后。这些 PDS3 表型特征在大量批量和单细胞数据集中很明显，并区分了一系列微妙的生物状态，这些状态目前在临床前模型中代表性不足，并且无法使用现有的亚型分类器进行识别。