The pH-dependent adaptive advantage for recurrent histidine mutations in cancer

描述（由申请人提供）：pH失调是几乎所有癌症的标志，无论其组织起源或遗传背景如何。在正常细胞中，细胞外pH值（pHe）高于细胞内pH值（pHi），但在癌细胞中，这种pH梯度是相反的。虽然pHi的本构性增加很小，但它会产生细胞功能的实质性变化。例如，癌细胞pHi的升高促进了细胞的增殖和侵袭，同时抑制了细胞凋亡，改变了细胞代谢。在这里，我们建议研究癌症中的体细胞突变，这些突变可能会增加对癌症失调pH值的适应性。虽然癌症中的体细胞突变是随机的，但癌症中pHi的增加可以为赋予适应性优势的突变提供选择压力。我们的假设是，这种选择压力导致癌症中组氨酸突变的保存，从而赋予pH敏感性的增加。为了研究这一假设，在目的1中，我们将确定候选蛋白中常见的Arg b>突变是否赋予pH依赖功能的增益，以及pH感知的机制可能是什么。对于每个候选蛋白，我们将通过体外和细胞内的生化测定来测试突变型而非野生型蛋白具有ph依赖性功能的预测。我们还将通过分子动力学模拟和计算pKa预测来测试突变体的pH感应机制。在目标2中，我们将使用数据库分析来识别具有重复组氨酸突变的其他候选者，确定其相对于密码子偏倚频率的频率，并生成相互作用网络来预测这些突变如何赋予癌细胞功能适应性优势。这些目标将通过使用资助人实验室从癌症体细胞突变目录（COSMIC）和已建立的生物信息学项目中生成的氨基酸突变数据库来实现。据我们所知，这是对癌症中涉及组氨酸的体细胞突变的适应性保留和ph依赖功能的第一次检查。我们的发现将对体细胞突变如何与癌症中失调的pH值联系起来产生新的见解。这项工作的结果也可能揭示pH传感器的广泛设计原则，可以为针对pH依赖性途径，调节机制或驱动突变的癌症治疗的发展提供信息。

DESCRIPTION (provided by applicant): Dysregulated pH is a hallmark of nearly all cancers regardless of tissue origin or genetic background. In normal cells, extracellular pH (pHe) is higher than intracellular pH (pHi) but in cancer cells this pH gradient is reversed. While the constitutive increase in pHi is small, it produces substantial changes in cell function. For example, the the increased pHi of cancer cells promotes cell proliferation and invasion while inhibiting apoptosis and altering cell metabolism. Here, we propose to investigate somatic mutations in cancer that may be conferring an increased fitness for the dysregulated pH of cancer. While somatic mutations in cancer are random, the increased pHi of cancers could provide a selective pressure for mutations that confer an adaptive advantage. Our hypothesis is that this selective pressure causes the conservation of histidine mutations in cancer that confer a gain in pH sensitivity. To investigate this hypothesis, in Aim 1 we will determine whether commonly occurring Arg>His mutations in candidate proteins confer a gain in pH-dependent function and what the mechanism of pH sensing might be. For each candidate we will test predictions that mutant but not wild- type proteins have pH-dependent functions by using biochemical assays in vitro and in cells. We also will test mechanisms of pH sensing of mutants by using molecular dynamics simulations and computational pKa predictions. In Aim 2 we will use database analyses to identify additional candidates with recurring histidine mutations, determine their frequency relative to codon bias frequency, and generate interaction networks to predict how these mutations might be conferring a functional adaptive advantage to cancer cells. These objectives will be achieved by using a database of amino acid mutations generated for the sponsor's laboratory from the Catalogue Of Somatic Mutations In Cancer (COSMIC) and established bioinformatics programs. To our knowledge this is the first examination of the adaptive retention and pH-dependent function of somatic mutations involving histidines in cancer. Our findings will generate new insights into how somatic mutations might be linked to the dysregulated pH in cancer. The results of this work might also reveal broad design principles of pH sensors that could inform the development of cancer therapeutics targeting pH-dependent pathways, regulatory mechanisms, or driver mutations.