【AACR2018】ExosomeDx公司通过血浆外泌体mRNA和lincRNA检测为乳腺癌患者免除组织活检
外泌体资讯网 讯/ Exosome Diagnostics公司的Sudipto Chakrabortty博士周二在芝加哥举行的AACR年会上展示了一项突破性的研究结果。液体活组织检查已经成为从血液或血浆等生物流体中获取肿瘤特异性信息的一种方式。由于每一个肿瘤都有独特的分子变化，监测这些血液样本变化而不进行侵入性组织活检的能力对于使患者获得最佳治疗非常重要。Exosome Diagnostics公司在此次AACR年会上展示的数据是一个意想不到的飞跃，该研究显示能够通过血液检测乳腺癌组织的独特RNA谱，而不需要组织样本。
外泌体是从肿瘤细胞和正常细胞中主动分泌的小囊泡，含有释放它的细胞的所有信息，包括RNA和蛋白质。生物流体，如血液或血浆，非常复杂，含有来自肿瘤和身体正常过程的物质。该研究使用乳腺癌特异性标记物从血液中分离乳腺癌特异性外泌体，并使用RNAseq分析来自样品的总RNA成分。研究人员还对来自这些患者的匹配FFPE组织样品的RNA进行了测序。
“实验结果非常令人兴奋。我们不仅可以准确地从血浆样本中鉴定乳腺癌RNA特征，而且我们甚至可以看到来自患者的乳腺癌外泌体与其匹配的FFPE组织样本的特征完全相符。考虑到每位患者都是独一无二的，这一结果相当完美，”Exosome Diagnostics首席科学官Johan Skog说。
“我们以前的研究表明，与无细胞DNA分析相比，我们可以通过将外泌体RNA和无细胞DNA相结合来提高突变检测的性能，但是这项癌症特异性外泌体富集的研究具有更重要的革新意义。这种能力（Exosome的专利EDDE技术）使我们能够从1 mL血浆中检测来自组织的实际RNA特征，避免了组织分析肿瘤特异性RNA变化的需要。与组织样本一致，我们在外泌体中检测到了相同的RNA广度和多样性，拥有超过12,000种不同的mRNAs和1000多种lincRNAs。乳腺癌特异性外泌体与匹配的组织的特征几乎完全相同。但在没有富集的情况下对血浆外泌体进行测序时无法得到此结果。实现这一飞跃也并非一帆风顺，Exosome Diagnostics多年来一直在研究如何从生物流体中最大程度地富集组织特异性外泌体，这是EDDE平台拥有的专利方法，”Dr. Skog继续说道。
Exosome Diagnostics总裁兼首席执行官John Boyce说，“Johan Skog博士开创了外泌体研究领域的领先地位，并且在Exosome Diagnostics十多年来建立了完善的分析方法学，能够分析尿液和血浆等生物流体中疾病特异性的RNA、DNA和蛋白质。通过使用这些专利方法（如EDDE）和专有的分析流程，Exosome Diagnostics可以实现非常低样本量的灵敏检测，而该领域的其他人却无法实现，”Boyce继续说。这种首次报道的数据证明Exosome Diagnostics的液体活检是免除组织活检和改善患者护理的解决方案。结合公司的人工智能在基因选择和商业渠道方面的能力，Exosome Diagnostics已经准备好改变医学领域。”
下面是Poster的具体内容：
The Poster Session at the AACR Annual Meeting 2018
LB-226 - Exosomal liquid biopsy reveals mRNA and lincRNA biomarkers in early stage breast cancer patient plasma
Author Block: S. K. Chakrabortty1, R. R. Kitchen1, C. M. Coticchia1, V. R. Tadigotla1, E. Eitan1, E. Castellanos-Rizaldos1, L. Bedford2, S. Badola2, M. D. Valentino1, N. Colafemina1, H. Uchiyama2, M. Morken1, M. Williams2, S. Vincent2, H. Danaee2, S. Yu1, J. Skog1;1ExosomeDx,Inc., Waltham, MA, 2Takeda Pharmaceuticals Intl. Co. Translational and Biomarker Res., Cambridge, MA
Introduction
Breast cancer is the most prevalent cancer in women, with approximately 250,000 diagnoses per year in the US. Non-invasive detection of breast cancer is of critical importance but has proven challenging due to the rate of false-positive diagnoses with current tests. Liquid biopsies including circulating tumor cells (CTCs) or cell-free DNA (cfDNA) have struggled with the detection of early stage disease. For example, a recent multi-analyte (cfDNA+protein) analysis, ‘cancerSEEK’, achieved a sensitivity of just 33% in breast cancer, highlighting the challenges facing the development of more sensitive and specific diagnostics for this disease.
Exosome-based liquid biopsy is a promising approach for minimally-invasive and highly sensitive diagnostics and it has been demonstrated that combining exosomal RNA and cfDNA greatly enhances mutation detection compared to profiling cfDNA alone. While most liquid biopsies profile mutations, studying RNA abundance in exosomes adds a new dimension to these non-invasive diagnostics. To date, much of the focus on exosomal RNA expression profiling has been on the small-RNA fraction. Here we demonstrate that whole-transcriptome profiling of mRNAs and lincRNAs greatly expands the landscape of potential biomarkers to clinically actionable genes.
Results
We have developed a novel platform designed to perform long-RNA sequencing on transcripts obtained from exosomes. We used this platform to compare expression profiles of total plasma exosomes versus subpopulations enriched for breast cancer-derived exosomes (CDE) versus depleted of non-cancer exosomes (NCE). The NCE-depleted and CDE-enriched exosomes equally outperformed total plasma exosomes, each detecting significantly more genes exhibiting breast cancer vs. healthy expression differences.
We performed NCE-depletion on 1.5 mL of input plasma from 15 stage I & II ER+/Her2- breast cancer patients and 12 healthy women matched for age & menopausal-status. RNA-seq data from these samples detected over 10,000 mRNAs and over 1,000 lincRNAs. Of these, we observed significantly increased abundance in over 100 mRNAs and lincRNAs in these early stage breast cancer patients. These mRNAs are enriched for gene-sets including those previously implicated in ‘breast cancer’, ‘chromatin remodeling’, and ‘immune response’.
We also performed RNA-seq on formalin-fixed paraffin-embedded (FFPE) samples from healthy and matched breast cancer tissue. The >100 genes found to be more abundant in breast cancer plasma exosomes significantly (p<0.05) separate the FFPE samples into two clusters corresponding to breast cancer patients and normal individuals, lending confidence to the exosomal signature.
Conclusions
This preliminary analysis highlights the exciting potential of exosomal long RNA based liquid biopsy for non-invasive early-stage detection of breast cancer. The platform is readily applicable to other disease areas and other biofluids such as urine or CSF.
编辑：企鹅
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