A Revised Molecular Model of Ovarian Cancer Biomarker CA125 (MUC16) Enabled by Long-read Sequencing.
A Revised Molecular Model of Ovarian Cancer Biomarker CA125 (MUC16) Enabled by Long-read Sequencing.
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DOI：
10.1158/2767-9764.crc-23-0327
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发表时间：
2024-01-31
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影响因子：
--
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中科院分区：
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生物标志物CA 125是一种位于粘蛋白MUC 16的几个串联重复序列中的肽表位，是监测高级别浆液性卵巢癌治疗后消退和复发的金标准。然而，CA 125表位沿着MUC 16分子的几个结构特征不明确。MUC 16中串联重复序列的数量以及这些重复序列中有多少含有CA 125表位仍然是未解决的一个中心问题。21世纪初的研究组装了短DNA读数，估计MUC 16含有63个重复。在这里，我们对来自三种原发性卵巢肿瘤和已建立的细胞系（OVCAR 3，OVCAR 5和Kuramochi）的MUC 16转录物进行纳米孔长读测序，以更详尽和准确地估计和测序MUC 16串联重复序列。来自这六个来源的共有序列通过蛋白质组学验证得到证实，并且与NCBI数据库中最近添加的一致。我们提出了一个模型MUC 16含有19-而不是63-串联重复。此外，我们使用深度学习算法AlphaFold预测串联重复结构域的结构。预测的结构显示了一个SEA域和非结构化的接头区富含脯氨酸，丝氨酸和苏氨酸残基的所有19个串联重复。这些研究现在为CA 125表位的详细表征铺平了道路。MUC 16串联重复序列的测序和建模沿着糖蛋白组学表征，目前正在我们的实验室进行，将有助于确定MUC 16分子中的新表位，提高目前CA 125检测的灵敏度和临床实用性。尽管它在卵巢癌的临床管理中起着至关重要的作用，但生物标志物CA 125的确切分子序列和结构尚未确定。在这里，我们结合联合收割机长读测序，质谱，并在电脑建模提供基础数据集的CA 125表位的更完整的表征。
The biomarker CA125, a peptide epitope located in several tandem repeats of the mucin MUC16, is the gold standard for monitoring regression and recurrence of high-grade serous ovarian cancer in response to therapy. However, the CA125 epitope along with several structural features of the MUC16 molecule are ill defined. One central aspect still unresolved is the number of tandem repeats in MUC16 and how many of these repeats contain the CA125 epitope. Studies from the early 2000s assembled short DNA reads to estimate that MUC16 contained 63 repeats. Here, we conduct Nanopore long-read sequencing of MUC16 transcripts from three primary ovarian tumors and established cell lines (OVCAR3, OVCAR5, and Kuramochi) for a more exhaustive and accurate estimation and sequencing of the MUC16 tandem repeats. The consensus sequence derived from these six sources was confirmed by proteomics validation and agrees with recent additions to the NCBI database. We propose a model of MUC16 containing 19—not 63—tandem repeats. In addition, we predict the structure of the tandem repeat domain using the deep learning algorithm, AlphaFold. The predicted structure displays an SEA domain and unstructured linker region rich in proline, serine, and threonine residues in all 19 tandem repeats. These studies now pave the way for a detailed characterization of the CA125 epitope. Sequencing and modeling of the MUC16 tandem repeats along with their glycoproteomic characterization, currently underway in our laboratories, will help identify novel epitopes in the MUC16 molecule that improve on the sensitivity and clinical utility of the current CA125 assay. Despite its crucial role in clinical management of ovarian cancer, the exact molecular sequence and structure of the biomarker, CA125, are not defined. Here, we combine long-read sequencing, mass spectrometry, and in silico modeling to provide the foundational dataset for a more complete characterization of the CA125 epitope.
影响因子：
5.6
作者：
Weiland F;Fritz K;Oehler MK;Hoffmann P
通讯作者：
Hoffmann P