Genetic and environmental determinants of age-acquired skewed X-inactivation and escape from X-inactivation

在人类中，女性携带两份X染色体，男性携带一条X和一条Y染色体。为了在两性之间保持一致的基因表达水平，在每个细胞中，女性都会使其两条X染色体中的一条保持沉默或“失活”。大多数雌性在每个细胞中随机地沉默一个X，因此在组织水平上，每个X被沉默的时间为50%。在功能上，这意味着同一身体中的细胞正在利用不同的DNA，这取决于给定细胞中哪条染色体被沉默。然而，随着女性年龄的增长，两个X染色体中的一个开始占据主导地位；在60岁以上的女性中，有35%的人在90%的细胞中有相同的X染色体沉默(称为倾斜X染色体失活)，而且优先沉默相同X染色体的女性比例随着年龄的增长而增加。目前尚不清楚这种与年龄相关的选择性沉默发生的原因，但它与癌症的生物标志物有关，并见于患有自身免疫性疾病的人，如系统性红斑狼疮和甲状腺疾病。有趣的是，双胞胎研究表明，与年龄相关的优先沉默是可遗传的，这表明一个人的基因与衰老过程相互作用，促进细胞沉默一个或另一个。在这项研究中，我们将研究与年龄相关的X染色体优先沉默的遗传学基础，以确定是什么遗传因素驱动了这一过程，以及相同的遗传因素是否与癌症和自身免疫性疾病的风险有关。随着英国人口老龄化，确定导致健康老龄化的因素并开发监测健康老龄化和预测未来疾病的生物标记物是公共卫生的优先事项。我们将探索优先沉默与衰老表型(如虚弱和发病率)之间的关系，以确定优先沉默是否可以作为女性健康衰老的生物标志物。沉默的(或“不活跃的”)X染色体上的一些基因仍然处于开启状态--它们逃脱了失活。沉默的X染色体上的基因在女性生物学中起着关键作用；只有一条X染色体的女性(因此绝对不表达第二条染色体上的基因)患有特纳斯综合征，包括各种器官系统的功能障碍。沉默的X基因表达的基因在女性中的剂量比男性高，这被认为是男性和女性疾病患病率差异的原因。例如，已知的几个逃脱X失活的基因是肿瘤抑制基因，来自沉默的X染色体的额外剂量具有保护作用--总体来说，女性比男性患癌症更少。相反，与女性偏向的自身免疫性疾病系统性红斑狼疮和类风湿性关节炎有关的几个基因是从沉默的X染色体表达的。在这种情况下，人们认为女性可能产生了太多的这些基因，从而使她们容易患上疾病。了解沉默X上的基因是如何受到控制的，以及这种基因在不同环境中是如何变化的，对于了解这些基因如何导致疾病至关重要。例如，组织受限逃逸将表明哪些组织对于介导基因对疾病的影响是重要的。目前估计，沉默的X基因上有12%-20%的基因可以被激活，它们的逃逸强度因个体而异。在这项研究中，我们将对X染色体上的基因进行深度测序，以确定哪些基因逃逸，逃逸的强度在不同的个体之间、同卵双胞胎之间(从而消除了因遗传而产生的变异性)以及跨组织之间是如何变化的。我们将重点关注与自身免疫性疾病相关的组织，因为这些组织与逃逸有关，以及在现有的血液、脂肪和皮肤的多组织数据集中寻找。最后，我们将研究逃逸如何随年龄变化，在自身免疫组织中横向变化，在全血数据集中纵向变化超过10年。

In humans, females carry two copies of the X chromosome and males one X and one Y chromosome. To maintain a consistent level of gene expression between the sexes, in every cell females silence or 'inactivate' one of their two X chromosomes. Most females randomly silence one X in each cell so that at a tissue level each X is silenced 50% of the time. Functionally, this means that cells in the same body are utilizing different DNA depending on which chromosome X is silenced in a given cell. However, as women age, one of the two X's starts to predominate; 35% of women over 60 have the same X chromosome silenced in >90% of their cells (termed 'skewed X-inactivation'), and the proportion of women with preferential silencing of the same chromosome X increases with age. It is not known why this age-associated preferential silencing happens, however it is associated with biomarkers of cancer and is seen in individuals with autoimmune diseases such as systemic lupus and thyroid disease. Intriguingly, twin-studies have shown that age-associated preferential silencing is heritable, suggesting an individual's genetics interact with the ageing process to promote cells silencing one X or the other. In this study we will investigate the genetic basis of age-associated chromosome X preferential silencing in order to determine what genetic factors drive this process and whether the same genetic factors are implicated in risk of cancer and autoimmune disease. As the UK population ages, it is a public health priority to identify factors that contribute to healthy ageing and develop biomarkers that monitor healthy ageing and predict future disease. We will explore the relationship between preferential silencing and ageing phenotypes such as frailty and disease incidence to determine if preferential silencing can act as a biomarker of healthy ageing in women. Some genes on the silenced (or 'inactive') X chromosome are still turned on - they escape inactivation. Genes on the silenced X have a critical role in female biology; women with only one X chromosome (and therefore absolutely no expression of genes from a second chromosome) have Turners syndrome, which includes dysfunction of various organ systems. Genes expressed from the silenced X have a higher dosage in females than males which is thought to underlie differences in disease prevalence between men and women. For example, several of the genes known to escape X-inactivation are tumor-suppressor genes and the extra dosage from the silenced X chromosome has a protective effect - overall women develop less cancer than men. Conversely, several genes implicated in the female-biased auto-immune diseases Systemic Lupus Erythematosus and Rheumatoid Arthritis are expressed from the silenced X chromosome. In this case, it is thought that women may produce too much of these genes which pre-disposes them to developing disease. Understanding how genes on the silenced X are controlled, and how this varies in different contexts, is critical to understanding how these genes contribute to disease. For example, tissue-limited escape would indicate which tissue is important for mediating a gene's effect on disease. It is currently estimated that 12-20% of genes on the silenced X can be turned on and that their strength of escape varies across individuals. In this study we will perform deep sequencing of the genes on chromosome X to determine which genes escape, how the strength of escape varies across unrelated individuals, between identical twins (thereby removing variability due to genetics), and across tissues. We will focus on autoimmune disease relevant tissues as these have been linked to escape, as well as looking in existing multi-tissue datasets of blood, fat and skin. Finally, we will investigate how escape varies with age both cross-sectionally in the autoimmune tissues and longitudinally over 10 years in a whole blood dataset.