Munro Matthew J, Wickremesekera Susrutha K, Tan Swee T, Peng Lifeng
School of Biological Sciences and Centre for Biodiscovery, Victoria University of Wellington, Wellington, 6140, New Zealand.
Gillies McIndoe Research Institute, Newtown, PO Box 7184, Wellington, 6242, New Zealand.
Clin Proteomics. 2022 Jul 16;19(1):27. doi: 10.1186/s12014-022-09364-y.
Colon cancer is the third most common cancer and second highest cause of cancer deaths worldwide. The aim of the study was to find new biomarkers for diagnosis, prognosis and therapeutic drug targets for this disease.
Four low-grade and four high-grade human colon adenocarcinoma tumours with patient-matched normal colon tissues were analysed. Additionally, tissue-derived primary cell lines were established from each tumour tissue. The cell lines were validated using DNA sequencing to confirm that they are a suitable in vitro model for colon adenocarcinoma based on conserved gene mutations. Label-free quantitation proteomics was performed to compare the proteomes of colon adenocarcinoma samples to normal colon samples, and of colon adenocarcinoma tissues to tissue-derived cell lines to find significantly differentially abundant proteins. The functions enriched within the differentially expressed proteins were assessed using STRING. Proteomics data was validated by Western blotting.
A total of 4767 proteins were identified across all tissues, and 4711 across primary tissue-derived cell lines. Of these, 3302 proteins were detected in both the tissues and the cell lines. On average, primary cell lines shared about 70% of proteins with their parent tissue, and they retained mutations to key colon adenocarcinoma-related genes and did not diverge far genetically from their parent tissues. Colon adenocarcinoma tissues displayed upregulation of RNA processing, steroid biosynthesis and detoxification, and downregulation of cytoskeletal organisation and loss of normal muscle function. Tissue-derived cell lines exhibited increased interferon-gamma signalling and aberrant ferroptosis. Overall, 318 proteins were significantly up-regulated and 362 proteins significantly down-regulated by comparisons of high-grade with low-grade tumours and low-grade tumour with normal colon tissues from both sample types.
The differences exhibited between tissues and cell lines highlight the additional information that can be obtained from patient-derived primary cell lines. DNA sequencing and proteomics confirmed that these cell lines can be considered suitable in vitro models of the parent tumours. Various potential biomarkers for colon adenocarcinoma initiation and progression and drug targets were identified and discussed, including seven novel markers: ACSL4, ANK2, AMER3, EXOSC1, EXOSC6, GCLM, and TFRC.
结肠癌是全球第三大常见癌症，也是癌症死亡的第二大原因。本研究的目的是寻找该疾病诊断、预后的新生物标志物以及治疗药物靶点。
分析了4例低级别和4例高级别人类结肠腺癌肿瘤及其配对的正常结肠组织。此外，从每个肿瘤组织建立了组织来源的原代细胞系。使用DNA测序对细胞系进行验证，以确认基于保守基因突变，它们是结肠腺癌合适的体外模型。进行无标记定量蛋白质组学分析，比较结肠腺癌样本与正常结肠样本的蛋白质组，以及结肠腺癌组织与组织来源细胞系的蛋白质组，以发现显著差异丰富的蛋白质。使用STRING评估差异表达蛋白质中富集的功能。蛋白质组学数据通过蛋白质印迹法进行验证。
在所有组织中共鉴定出4767种蛋白质，在原代组织来源细胞系中共鉴定出4711种蛋白质。其中，在组织和细胞系中均检测到3302种蛋白质。平均而言，原代细胞系与其亲本组织共享约70%的蛋白质，它们保留了关键结肠腺癌相关基因的突变，并且在遗传上与其亲本组织差异不大。结肠腺癌组织表现出RNA加工、类固醇生物合成和解毒上调，细胞骨架组织下调以及正常肌肉功能丧失。组织来源的细胞系表现出干扰素-γ信号增强和异常铁死亡。总体而言，通过比较高级别与低级别肿瘤以及两种样本类型的低级别肿瘤与正常结肠组织，318种蛋白质显著上调，362种蛋白质显著下调。
组织和细胞系之间表现出的差异突出了从患者来源的原代细胞系中可获得的额外信息。DNA测序和蛋白质组学证实，这些细胞系可被视为亲本肿瘤合适的体外模型。鉴定并讨论了多种结肠癌发生、发展的潜在生物标志物和药物靶点，包括7种新标志物：ACSL4、ANK2、AMER3、EXOSC1、EXOSC6、GCLM和TFRC。
