Novel Markers for Disease Outcome in Breast Cancer

项目1：我们继续全面检查非裔美国人和欧裔美国人乳腺癌患者的代谢组、蛋白质组和转录组，以发现生物标志物。这种方法的前景是发现预后的标记，以及可能导致非裔美国妇女乳腺癌侵袭的机制。我们描述了67例乳腺肿瘤和邻近非癌组织的代谢组学特征，并描述了200多种代谢物的差异丰度。其中之一是2-羟戊二酸，在雌激素受体主要为阴性的肿瘤中，其含量升高了100倍。2-羟戊二酸的积累与肿瘤中c-Myc信号信号的共同出现密切相关（PMID: 24316975）。在后续研究中，我们可以证明乳腺肿瘤主要积聚d -2-羟基戊二酸，并将d -2-羟基戊二酸产生醇脱氢酶含铁蛋白1 （ADHFE1）描述为与疾病生存相关的乳腺癌癌蛋白。我们的数据表明，ADHFE1促进还原性谷氨酰胺代谢，增加d -2-羟戊二酸和线粒体活性氧的形成（PMID: 29202474）。在这些代谢组学研究的延伸中，我们分析了乳腺肿瘤中胆汁酸的存在以及它们的积累与乳腺癌生物学的关系。这一探索性分析揭示了乳腺肿瘤的一个亚群积聚胆汁酸，并显示出独特的肿瘤生物学。胆汁酸含量高的肿瘤显示增殖率降低并与生存率提高相关（PMID: 31296531）。在另一项专注于乳腺癌蛋白质组的研究中，我们对乳腺肿瘤进行了综合蛋白质转录组学表征。我们测量了118个人类乳腺肿瘤和邻近非癌组织的整体蛋白质组和转录组表达。比较蛋白质组和转录组数据，我们发现蛋白质组描述了癌组织和非癌组织之间的差异，这些差异没有被转录组捕获。此外，蛋白质组和转录组强调了部分不同的肿瘤生物学。当我们应用这两种技术的综合分析时，该方法揭示了肿瘤中蛋白质- mrna一致性的全球增加。高度相关的蛋白质基因对在蛋白质加工和疾病代谢途径中富集，并且在非裔美国患者的肿瘤中更常见。转录物和蛋白水平之间的一致性增加与侵袭性疾病（包括基底样/三阴性肿瘤）和患者生存率降低进一步相关。我们的研究表明，对癌症中蛋白质组和转录组的综合分析可以揭示超出单一技术能力的疾病特征。这些数据已于2018年发布（PMID: 30501643）。项目2：环境暴露和肥胖可以改变DNA甲基化模式，改变肿瘤表观基因组，如前列腺癌和乳腺癌。我们目前的研究调查了人类乳腺组织中全基因组DNA甲基化与年龄、体重指数、组织炎症、人口群体和邻里剥夺措施的关系。在这里，我们将NCI- maryland合同资源与Gierach实验室（DCEG/NCI）从Komen组织库获得的补充资源相结合。这一伙伴关系将包括来自大约1000名妇女的全基因组DNA甲基化数据。NCI-Maryland队列的独特之处在于，我们可以将DNA甲基化模式与该人群的邻里剥夺指数、乳腺癌和糖尿病诊断联系起来。Komen组织库队列包括年龄匹配的非裔美国人和欧裔美国人，未患乳腺癌的绝经前捐赠者。这些女性通过缩胸手术提供了非癌性乳腺组织。我们将研究这些组织中的DNA甲基化和组织炎症标记物，来自NCI-Maryland队列的其他乳房缩小组织，以及从尸检病例中获得的正常乳房组织。本研究将补充来自非裔美国人和欧洲裔美国患者的乳腺肿瘤邻近非癌组织对的DNA甲基化数据。此次合作的主要目的是评估全基因组DNA甲基化模式与组织炎症标志物（如冠状结构和其他风险因素）、非裔美国人和欧裔美国女性之间的差异、糖尿病和邻里剥夺措施对DNA甲基化的影响，以及研究非裔美国人和欧裔美国女性癌症组织和非癌组织之间的差异。DNA甲基化数据也可以与许多这些组织的现有基因表达数据集集成。项目3：该项目评估环境诱导的应激信号和合并症在乳腺癌进展中的作用。我们开始研究生活压力事件和糖尿病对肿瘤生物学的影响。在一项临床研究中，我们将对计划进行乳腺癌手术的乳腺癌患者进行一项简短的调查，评估他们感受到的压力和社会孤立。我们还将收集这些患者的冷冻肿瘤和邻近正常乳腺组织和血液样本，并评估乳腺组织或血液样本是否具有与他们感知的压力和社会孤立状态相关的生物学特征。我们假设，高感知压力暴露的患者具有与更具侵袭性疾病和较差生存率一致的生物学特征。该试点研究的目的是从同意的患者中收集100对肿瘤/正常配对，并完成调查。在第二项研究中，我们正在评估自我报告的糖尿病与肿瘤生物学和乳腺癌侵袭性之间的关系。在这里，基于调查和医疗记录数据的患者糖尿病状态将与肿瘤中的整体基因表达、代谢物模式和突变特征相关联，以确定受糖尿病影响的癌症相关途径。这项研究正在进行中，将评估1型和2型糖尿病是否会诱导肿瘤生物学的变化，从而提高疾病进展的几率。我们特别感兴趣的是代谢途径的变化，以及如何针对它们来减少糖尿病诊断对乳腺癌结果的负面影响。更具体地说，我们正在研究糖尿病对乳腺癌生物学的影响，采用三管齐下的方法，包括分析原位人类肿瘤异种移植物、患者肿瘤和暴露于糖尿病/高血糖样条件下的乳腺癌细胞。目前的研究结果如下：糖尿病不增强细胞增殖，但诱导间充质和干细胞样表型，与移动性和转移几率增加有关。它还促进了氧自由基的形成以及DNA修复缺陷的转录组和突变特征。此外，食物和微生物衍生的代谢物倾向于在糖尿病患者的乳腺肿瘤中积累，潜在地影响肿瘤生物学。在高血糖样条件下培养的乳腺癌细胞获得了更多的DNA损伤和对DNA修复抑制剂的敏感性。基于这些观察，糖尿病相关乳腺肿瘤对DN的药物反应可能会增加

Project 1: We continued to comprehensively examine the metabolome, proteome, and transcriptome of breast tumors from African American and European-American patients for biomarker discovery. The promise of this approach is the discovery of markers for prognosis, and of mechanisms that may drive the aggressiveness of breast cancer in African American women. We characterized the metabolomic profile of breast tumors and adjacent non-cancerous tissue from 67 patients and described the differential abundance of more than 200 metabolites. One of them was 2-hydroxyglutarate, which was elevated up to 100-fold in tumors that were primarily estrogen receptor-negative. This accumulation of 2-hydroxyglutarate was closely associated with the co-occurrence of a c-Myc signaling signature in the tumors (PMID: 24316975). In a follow up study, we could show that breast tumors predominately accumulate D-2-hydroxyglutarate and describe the D-2-hydroxyglutarate-producing alcohol dehydrogenase, iron-containing protein 1 (ADHFE1) as a breast cancer oncoprotein that is associated with disease survival. Our data show that ADHFE1 promotes a reductive glutamine metabolism with increased D-2-hydroxyglutarate and mitochondrial reactive oxygen species formation (PMID: 29202474). In an extension to these metabolome studies, we analyzed breast tumors for presence of bile acids and how their accumulation may relate to breast cancer biology. This exploratory analysis revealed that a subset of breast tumors accumulates bile acids and show a distinct tumor biology. Tumors with a high bile acid content showed a decreased proliferation rate and associated with improved survival (PMID: 31296531). In a different study, focusing on the breast cancer proteome, we performed an integrated proteotranscriptomic characterization of breast tumors. We measured global proteome and transcriptome expression in 118 human breast tumors and adjacent non-cancerous tissues. Comparing proteome with transcriptome data, we found that the proteome describes differences between cancerous and non-cancerous tissue that are not captured by the transcriptome. Moreover, the proteome and transcriptome highlighted partially different tumor biologies. When we applied an integrated analysis of both technologies, the approach revealed a global increase in protein-mRNA concordance in tumors. Highly correlated protein-gene pairs were enriched in protein processing and disease metabolic pathways and occurred more commonly in tumors of African American patients. The increased concordance between transcript and protein levels was further associated with aggressive disease, including basal-like/triple-negative tumors, and decreased patient survival. Our study indicates that an integrated analysis of the proteome and transcriptome in cancer can uncover disease characteristics beyond the ability of a single technology. These data have been published in 2018 (PMID: 30501643). Project 2: Environmental exposures and obesity can modify DNA methylation patterns and alter the tumor epigenome, as shown for prostate and breast cancer. Our current research investigates genome-wide DNA methylation in human breast tissues in association with age, body mass index, tissue inflammation, population group, and neighborhood deprivation measures. Here, we are combining the resources from the NCI-Maryland contract resource with a complementary resource acquired by the Gierach laboratory (DCEG/NCI) from the Komen tissue bank. This partnership will encompass genome-wide DNA methylation data from about one thousand women. It is the unique aspect of the NCI-Maryland cohort that we can link DNA methylation pattern to the neighborhood deprivation index, breast cancer, and the diagnosis of diabetes in this population. The Komen tissue bank cohort consists of African American and European American age-matched, pre-menopausal donors without breast cancer. These women provided non-cancerous breast tissue from breast reduction surgery. We will study DNA methylation and tissue inflammation markers in these tissues, additional breast reduction tissues from the NCI-Maryland cohort, and in normal breast tissues obtained from autopsy cases. This study will be supplemented with DNA methylation data from breast tumor-adjacent non-cancerous tissue pairs from African American and European American patients. It is the main aim of this collaboration to evaluate patterns of genome-wide DNA methylation in association with tissue inflammation markers like crown-like structures and other risk factors, differences between African American and European-American women, the impact of diabetes and neighborhood deprivation measures on DNA methylation, and to study differences between cancerous and non-cancerous tissues in African American and European-American women. The DNA methylation data can also be integrated with existing gene expression data sets for many of these tissues. Project 3: This project evaluates the role of environmentally induced stress signaling and co-morbidities in breast cancer progression. We started projects studying the impact of stressful life events and diabetes on tumor biology. In a clinical study, we will give breast cancer patients, who are scheduled for breast cancer surgery, a short survey evaluating their perceived stress and social isolation. We will also collect frozen tumor and adjacent normal breast tissue and blood samples from these patients and evaluate whether the breast tissue or the blood samples have a biological signature related to their perceived stress and social isolation status. We hypothesize that patients with a high perceived stress exposure have a biological signature consistent with a more aggressive disease and poorer survival. The pilot study is designed to collect 100 tumor/normal pairs from consented patients with a completed survey. In a second study, we are evaluating the relationship between self-reported diabetes and tumor biology and breast cancer aggressiveness. Here, a patient's diabetes status based on survey and medical record data will be correlated with global gene expression, metabolite patterns, and mutational signatures in their tumors to identify cancer-related pathway that are impacted by diabetes. This study is ongoing and will assess whether type 1 and 2 diabetes induce changes to tumor biology that enhance the odds of disease progression. We are particularly interested in changes to metabolic pathways, and how they can be targeted to decrease the negative impact that a diabetes diagnosis may have on breast cancer outcomes. More specifically, we are investigating the influence of diabetes on breast cancer biology using a three-pronged approach that includes analysis of orthotopic human tumor xenografts, patient tumors, and breast cancer cells exposed to diabetes/hyperglycemia-like conditions. Current findings are as follows: Diabetes did not enhance cell proliferation but induced mesenchymal and stem cell-like phenotypes linked to increased mobility and odds of metastasis. It also promoted oxyradical formation and both transcriptome and mutational signatures of DNA repair deficiency. Moreover, food- and microbiome-derived metabolites tended to accumulate in breast tumors in presence of diabetes, potentially affecting tumor biology. Breast cancer cells cultured under hyperglycemia-like conditions acquired increased DNA damage and sensitivity to DNA repair inhibitors. Based on these observations, diabetes-associated breast tumors may show an increased drug response to DN *TRUNCATED*