Laura E. Kane, Croí E. Buckley, Rebecca M. O'Brien, Meghana S. Menon, Aisling B. Heeran, Xiaofei Yin, Timothy S. Nugent, Noel E. Donlon, John V Reynolds, Adnan Hafeez, Diarmuid S. O'Ríordáin, Robert A. Hannon, Paul Neary, Reza Kalbassi, Brian J. Mehigan, Paul H. McCormick, Cara Dunne, John O. Larkin, Lorraine Brennan, Michael E. Kelly, Jacintha O'Sullivan, Niamh Lynam-Lennon
<p>Dear Editor,</p><p>Rectal cancer (RC) incidence is rising, particularly in individuals < 50 years, who present with aggressive, treatment-refractory tumours.<span><sup>1</sup></span> Resistance to neoadjuvant treatment (neo-tx) is a significant problem, with no biomarkers of response currently in use. Tumours of similar clinical characteristics can have vastly different responses to neo-tx, suggesting the dichotomy in response is due to differences in the tumour molecular environment. Alterations in mitochondrial function and energy metabolism play a role in the pathogenesis of gastrointestinal cancers,<span><sup>2, 3</sup></span> implicating the metabolome as a potential untapped source of predictive biomarkers. To address this unmet need, we performed multi-omic analysis of metabolomic and transcriptomic profiles from normal, non-cancer rectal tissue and pre-treatment RC biopsies (Supporting Information) to identify alterations associated with the pathogenesis of RC.</p><p>Liquid chromatography-mass spectrometry revealed 29 metabolites significantly altered in RC tissue (<i>n </i>= 32) compared to non-cancer rectal tissue (<i>n </i>= 20) (Figure 1A). Pathway analysis uncovered 65 upregulated and four downregulated pathways significantly associated with altered metabolites (Figure 1B). Most altered metabolites were lipid molecules or mediators of lipid metabolism, suggesting that remodelling of lipid metabolism is a feature of RC. Diacyl phosphatidylcholines (PCs) are important mediators of lipid metabolism, supporting other studies highlighting a role for choline metabolism and lipid remodelling in tumourigenesis.<span><sup>4</sup></span> SM C18:0 and SM (OH) C22:1 are sphingolipids, important structural lipid components of biological membranes, which support the physiological function of the colon and are deregulated in RC.<span><sup>5</sup></span> Interestingly, cancer cells hydrolyse sphingomyelin to maintain production of PCs,<span><sup>4</sup></span> suggesting a mechanism for the concomitant increase in PCs and decrease in sphingomyelins demonstrated in RC here.</p><p>Real-time metabolic analysis demonstrated that (Figure 1C)OCR rates and OCR/ECAR ratios were significantly decreased in RC compared to non-cancer rectal tissue, highlighting metabolic remodelling in RC. Inhibition of mitochondrial metabolism results in accelerated turnover of PCs in neuronal cells,<span><sup>6</sup></span> suggesting a mechanism underlying the altered choline metabolism demonstrated in RC.</p><p>Transcriptomics revealed 2337 genes differentially expressed between RC (<i>n </i>= 31) and non-cancer rectal tissue (<i>n </i>= 28) (Figure 1D). Pathway analysis revealed 41 upregulated and seven downregulated pathways significantly associated with altered genes (Figure 1E). Interestingly, several of the most altered genes play roles in mitochondrial respiration. <i>ND2</i>, <i>ND3</i> and <i>ND5</i> encode subunits of the NADH dehydrogenase enzyme, a crucial
亲爱的编辑,直肠癌(RC)的发病率正在上升,特别是在50岁以上的个体中,他们表现出侵袭性,难治性肿瘤对新辅助治疗(neo-tx)的耐药是一个重要的问题,目前还没有生物标志物的反应。临床特征相似的肿瘤可能对neo-tx有截然不同的反应,这表明反应的二分法是由于肿瘤分子环境的差异。线粒体功能和能量代谢的改变在胃肠道癌症的发病机制中发挥作用,2,3暗示代谢组是一种潜在的未开发的预测性生物标志物来源。为了解决这一未满足的需求,我们对正常、非癌性直肠组织和治疗前直肠癌活检的代谢组学和转录组学进行了多组学分析,以确定与直肠癌发病机制相关的改变。液相色谱-质谱分析显示,与非癌直肠组织(n = 20)相比,癌组织中有29种代谢物显著改变(n = 32)(图1A)。通路分析发现65条上调通路和4条下调通路与代谢产物改变显著相关(图1B)。大多数改变的代谢物是脂质分子或脂质代谢介质,这表明脂质代谢的重塑是RC的一个特征。二酰基磷脂酰胆碱(PCs)是脂质代谢的重要介质,支持其他研究强调胆碱代谢和脂质重塑在肿瘤发生中的作用SM C18:0和SM (OH) C22:1是鞘脂,是生物膜的重要结构脂质成分,支持结肠的生理功能,在RC中不受调节。有趣的是,癌细胞水解鞘磷脂以维持pc的产生,这表明在RC中证明了pc同时增加和鞘磷脂减少的机制。实时代谢分析显示(图1C),与非癌性直肠组织相比,癌性直肠组织的OCR率和OCR/ECAR比值显著降低,突出了癌性直肠组织的代谢重塑。线粒体代谢的抑制导致神经元细胞中pc的更新加速,6这表明在RC中证实了胆碱代谢改变的机制。转录组学显示,有2337个基因在直肠癌组织(n = 31)和非癌直肠组织(n = 28)之间存在差异表达(图1D)。通路分析显示41条上调通路和7条下调通路与基因改变显著相关(图1E)。有趣的是,一些改变最多的基因在线粒体呼吸中起作用。ND2, ND3和ND5编码NADH脱氢酶的亚基,NADH脱氢酶是电子传递链的关键组成部分,支持在RC组织中显示的改变的OCR。在治疗前的RC活检中,改变的代谢物与OCR、ECAR、OCR/ECAR比值以及几个临床变量(包括改进的Ryan肿瘤反应评分(TRS))有显著相关性(TRS1 =完全缓解,TRS1 =接近完全缓解,TRS2 =部分缓解)(图2A)。两种代谢物与TRS显著相关:血清素和lysoPC a C16:1(图2B)。无监督分层聚类在TRS2中显示出良好的分组,TRS0和TRS1之间几乎没有区别,表明两者之间的表达谱相似(图2C)。只有lysoPC a C16:1与临床变量有显著相关性(图2D)。SLC6A4在CRC组织中的表达,其转录5 -羟色胺,对无复发生存无显著影响(图2E),而SLC6A4的低表达导致进展后生存显著恶化(图2F)。5 -羟色胺可增强结肠癌患者的放射敏感性,7提示TRS2患者血清素降低是neo-tx耐药的机制之一。改变的基因与几个临床变量有显著相关性(图3A)。RPL30和CXCL14在TRS2中显著上调,而SNORA81、SNORD50A、LCN2和SNORA64在TRS2中与TRS0相比显著下调(图3B)。RPL30的表达增加与癌基因MYC的扩增有关,从而促进细胞毒性治疗的耐药性在一些癌症中,SNORD50A的缺失与较差的生存结果相关有趣的是,SNORD50A结合并抑制癌基因KRAS, SNORD50A的耗尽导致MAPK级联的激活,9参与肿瘤对治疗的耐药,10提示在RC中neo-tx耐药的潜在作用。基于基因表达的TRS分离得到了改进,TRS0和TRS2区分明显(图3C)。一些基因与临床变量有显著相关性(图3D)。低CXCL14表达与总体(图3E)和进展后生存期(图3F)明显较差相关。 高RPL30与较长的总生存期显著相关(图3G);然而,它导致无复发生存(图3H)和进展后生存(图3I)显著恶化,这与TRS2患者的高RPL30一致。同样,低LCN2表达与较差的总生存率相关(图3J)。改变的基因和代谢物被整合到一个8个特征的多组学生物标志物面板中。由于没有匹配的TRS3患者转录组数据,只有TRS0 (n = 3)、TRS1 (n = 6)和TRS2 (n = 5)组可以纳入最终分析。TRS0和TRS2分别使用这8个特征进行聚类,TRS1分布在它们之间(图4A)。主成分分析显示了类似的模式,血清素、SNORA64、SNORD50A、SNORA81、RPL30和CXCL14对组分离的贡献最大(图4B)。单独检查各特征的表达情况,TRS0和TRS2的单独特征表达水平较高,而TRS1位于TRS0和TRS2的范围内(图4C)。留一交叉验证表明,TRS0与TRS1/TRS2的区别较差(曲线下面积[AUC] = 0.273,灵敏度= 0%,特异性= 54.5%),可能是由于组间样本的不平衡(TRS0 = 3, TRS1/TRS2 = 11),因此不能准确地代表这些组间面板的性能(图4D)。与TRS2相比,TRS0的分类准确率要高得多(AUC = 0.933,灵敏度= 100%,特异性= 80%),这与观察到的不同表达谱一致(图4B,C)。最后,在该试点队列中,TRS0/TRS1与TRS2表现出完美的分类(AUC = 1, Sensitivity = 100%, Specificity = 100%),表明总体而言,TRS2患者的表达谱与TRS0和TRS1不同,两者之间的关系更为密切(图4D)。在一个试点队列中,我们证明直肠肿瘤具有代谢和转录组重塑,强调脂质代谢改变是直肠肿瘤的共同特征,提出了一种新的治疗靶向方法。我们还确定了一个新的多组学8-生物标志物面板,在代表全TRS谱的独立队列验证后,有潜力作为neo-tx病理反应的预测标志,以改善患者分层。劳拉e凯恩:数据策展,正式分析和写作-原始草案。Croí E. Buckley:调查,数据管理和形式分析。丽贝卡·M. o .布莱恩:数据管理和资源。Meghana S. Menon:数据管理和资源。Aisling B. Heeran:数据管理和资源。尹晓飞:调查与形式分析。Timothy S. Nugent:临床样本和临床数据。Noel E. Donlon:临床样本和临床数据。约翰·v·雷诺兹:资源。Adnan Hafeez:临床样本。Diarmuid S. O.R-ordáin:临床样本。Robert A. Hannon:临床样本。Paul Neary:临床样本。Reza Kalbassi:临床样本。Brian J. Mehigan:临床样本。Paul H. McCormick:临床样本。卡拉·邓恩:临床样本。John O. Larkin:临床样本。洛林·布伦南:形式分析和写作——审查和编辑。迈克尔E.凯利:临床样本,临床数据和写作-审查和编辑。贾辛塔O.沙利文:概念,监督和写作-审查和编辑。概念化、监督、资金获取、写作。原稿和写作-审查和编辑。作者声明无利益冲突。这项研究由卫生研究委员会(爱尔兰)资助,资助号:EIA-2017-020。我们也感谢SFI研究基础设施计划下的综合分子分析平台(CMAP)的资助,参考编号:18/RI/5702。勒。凯恩得到了爱尔兰研究基
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