Molecular Subtypes of Human Skeletal Muscle in Cancer Cachexia

Cancer-associated muscle wasting associates with poor clinical outcomes1, but its underlying biology is largely uncharted in humans2. Unbiased RNAome analysis (coding and non-coding RNAs) with unsupervised clustering using Integrative Non-negative Matrix Factorization (intNMF)3 provides an avenue to identify distinct molecular subtypes, here applied to muscle of patients with colorectal or pancreatic cancer. Rectus abdominis biopsies from 84 patients was profiled using high-throughput next generation sequencing. Here we show that intNMF with stringent quality metrics of clustering identifies 2 highly coherent molecular subtypes within muscle of patients with cancer. Patients in Subtype 1 (vs Subtype 2) showed clinical manifestations of cachexia: high-grade weight loss, low muscle mass, atrophy of Type IIA and Type IIX muscle fibres and reduced survival. Based on differential expression between the subtypes, our results indicate biological processes that may contribute to cancer-associated loss of muscle mass and function, including altered post-transcriptional regulation, and perturbation of neuronal systems, cytokine storm/cellular immune response, extracellular matrix, and metabolic abnormalities spanning xenobiotic metabolism, hemostasis, signal transduction, embryonic/pluripotent stem cells, and amino acid metabolism. Differential expression between subtypes indicates involvement of multiple, intertwined higher-order gene regulatory networks, suggesting potential for interacting (hub)lncRNA-miRNA-mRNA interaction networks as targets for future research.肿瘤相关肌肉消耗（Cancer-associated muscle wasting）与不良临床结局¹密切相关，但其在人体中的潜在生物学机制迄今尚未得到充分阐明²。采用整合非负矩阵分解（Integrative Non-negative Matrix Factorization, intNMF）进行无监督聚类的无偏转录组（RNAome）分析（涵盖编码RNA与非编码RNA）³，为鉴定独特的分子亚型提供了可行途径，本研究将该方法应用于结直肠癌或胰腺癌患者的肌肉组织。本研究对84例患者的腹直肌活检样本开展了高通量下一代测序分析。结果显示，采用严格聚类质量指标的intNMF分析，可在癌症患者的肌肉组织中鉴定出2个高度一致的分子亚型。1型亚型（相较于2型亚型）患者表现出恶病质的临床特征：重度体重丢失、肌肉量降低、IIA型与IIX型肌纤维萎缩，以及生存期缩短。基于亚型间的差异表达谱，本研究结果揭示了可能参与肿瘤相关肌肉质量与功能丧失的生物学过程，包括转录后调控异常、神经系统扰动、细胞因子风暴/细胞免疫应答、细胞外基质异常，以及涵盖异生物质代谢、止血、信号转导、胚胎/多能干细胞相关进程与氨基酸代谢在内的代谢紊乱。亚型间的差异表达提示，多个相互交织的高阶基因调控网络参与其中，这表明以相互作用型（枢纽）长链非编码RNA（long non-coding RNA, lncRNA）-微小RNA（microRNA, miRNA）-信使RNA（messenger RNA, mRNA）相互作用网络作为未来研究靶点具备潜在价值。