Understanding the effect of mutations on cell behaviour in blood disorders through mathematical modelling and computational analysis

克隆性扩增在造血学，即血细胞的生产中研究得尤其深入。克隆性造血(CH)是在健康老年人的血液或骨髓中检测到的造血干细胞(HSCs)突变的扩大。65岁以上人口中有超过10%的人患有先天性心脏病。先天性心脏病与全因死亡率、心脏病和缺血性中风的风险增加有关。2022年，CH已被世界卫生组织确认为前驱髓系疾病状态。CH是骨髓增生异常综合征(MDS)的已知危险因素，MDS是一组血癌，骨髓中的血液干细胞成熟及其下游分化血细胞的产生受到损害。剪接体成分的突变，其中SF3B1是最常见的事件之一，在驱动克隆性扩张和疾病进展方面发挥着重要作用。此外，SF3B1是一种特别有趣的遗传驱动因素，因为它具有双重风险，在环状铁粒母细胞(MDS-RS)的MDS中构成保护性事件，但在5q缺失的MDS中共存时预后很差。目前尚不清楚这些不同影响的原因以及不同SF3B1突变在MDS扩展和进展中的作用。目前，Risk预后是作为诊断测序方法的一部分来计算的，很少有研究集中于随着时间的推移是什么因素驱动克隆性扩展。能够预测不同突变的克隆性扩展并了解共突变如何相互作用来改变疾病风险，可以促进对个体MDS的监测，以进行风险分层。需要更多的研究来确定某些克隆在骨髓和血液生产中能够胜过其他克隆的机制。舒马赫研究小组最近表明，不同基因的突变可以有不同的扩张率。这一洞察力来自健康老年人的纵向测序数据的可用性，结合克隆扩展的数学模型来理解这些数据。我们现在计划应用这种方法来量化和了解MDS中SF3B1突变的克隆性扩展。由于带有SF3B1突变的MDS的风险通常较低，它们比其他血液恶性肿瘤更接近CH的癌前状态，因此我们的方法可能只需进行很小的修改即可适用。Hellström Lindberg小组建立了一个注释良好的生物库&gt；1200名MDS及相关疾病患者。该小组的一个重点是带有SF3B1基因突变的MDS，他们会随着时间的推移对其进行连续采样。这些数据为扩展最近的数学模型的适用性提供了理想的试验台，由Hellström Lindberg小组的临床专业知识指导。该小组还建立了3D培养系统，以研究具有已知突变的患者来源细胞的体外克隆扩增。我们将系统地量化选定的SF3B1突变的扩展动力学和可变性。这将作为体内发现的验证，并使数学模型的进一步发展能够包括克隆扩张的不同潜在机制，其预测可以通过实验进行验证。调整克隆性造血的数学模型，使其适用于低风险MDS患者的数据。测试SF3B1突变的克隆性扩张率是否特定于突变变体、基因内的热点位置或其他因素(例如，来自临床元数据)。用3D培养系统验证克隆扩增的差异，并量化动力学的变异性。调整数学模型，使其适用于3D培养系统的体外数据。使用体外实验和数学模型相结合的方法，确定SF3B1突变如何导致克隆扩张的机制。

Clonal expansion is particularly well studied in haematopoiesis, the production of blood cells. Clonal haematopoiesis (CH) is the expansion of mutations in haematopoietic stem cells (HSCs) that become detectable in blood or bone marrow of healthy aged individuals. More than 10% of the population over 65 years of age are affected by CH. CH is associated with increased risk for all- cause mortality, heart disease and ischaemic stroke. In 2022, CH has been recognised by the World Health Organization as a precursor myeloid disease state.CH constitutes a known risk factor for myelodysplastic syndromes (MDS), a group of blood cancers in which the maturation of blood stem cells in the bone marrow and their downstream production of differentiated blood cells is impaired. Mutations in spliceosome components, with SF3B1 as one of the most common events, play a significant role in driving clonal expansion and disease progression. Additionally, SF3B1 is a particularly interesting genetic driver due to its dual risk profile, constituting a protective event in MDS with ring sideroblasts (MDS-RS) and yet having a dismal prognosis when co- occurring in MDS with 5q deletion. The reasoning for these distinct effects and the role of different SF3B1 mutations in MDS expansion and progression are currently unknown.Risk prognosis is currently calculated as part of a diagnostic sequencing approach, with few studies centred on what factors drive clonal expansion over time. Being able to predict the clonal expansion of different mutations and understanding how co-mutations interact to modify disease risk could facilitate monitoring of MDS in individuals for the stratification of risk. More research is required to determine the mechanisms by which certain clones can outcompete others in the bone marrow and blood production.The Schumacher group has recently shown that mutations in different genes can have different expansion rates. This insight was enabled by the availability of longitudinal sequencing data from healthy aged individuals in combination with mathematical models of clonal expansion to make sense of such data. We now plan to apply this approach to quantify and understand the clonal expansion of SF3B1 mutations in MDS. As MDS with SF3B1 mutations are typically lower risk they are closer to the pre-malignant status of CH than other blood malignancies and therefore our methods may be applicable with only small modifications.The Hellström Lindberg group has established a well-annotated biobank of >1200 consecutive patients with MDS and related disorders. One focus of the group lies on MDS with mutations in the gene SF3B1, for which they do serial sampling over time. These data provide the ideal test-bed for extending theapplicability of recent mathematical models, guided by the clinical expertise of the Hellström Lindberg group. The group has also established a 3D culture system to study the clonal expansion of patient-derived cells with known mutations in vitro. We will systematically quantify the kinetics and variability of expansion of selected SF3B1 mutations. This will serve as validation of the in vivo findings and enable the further development of mathematical models to include different potential mechanisms of clonal expansion, the predictions of which can be tested experimentally.Aims1. Adapt mathematical models of clonal haematopoiesis to make them applicable to data from low risk MDS patients.2. Test whether rate of clonal expansion of SF3B1 mutations is specific to the mutational variant, hotspot location within the gene, or other factors (e.g., from clinical metadata).3. Verify differences in clonal expansion using 3D culture system and quantify variability of kinetics.4. Adapt mathematical models to make them applicable to in vitro data from 3D culture system.5. Determine the mechanism of how SF3B1 mutations cause clonal expansion using a combination of in vitro experiments and mathematical models.