Characterizing the effects of cis-regulatory variation on patient outcomes and treatment response in Multiple Myeloma

摘要 多发性骨髓瘤（MM）是浆细胞恶性肿瘤，是第二常见的血液系统癌症 占癌症死亡人数的2%。MM与不良预后相关，虽然新的治疗方法 尽管存活率有所提高，但大多数患者仍会复发。MM表现出很强的遗传性 由于MM患者的亲属具有2至4倍的疾病发展风险，因此，此外，委员会认为， MM的发生率和死亡率在性别之间存在差异，男性的风险高于女性。 全基因组关联研究（GWAS）确定了许多与MM易感性相关的风险位点， 元分析位于调控区内或附近，表明转录调控中的作用。 调控然而，这些风险位点如何促进肿瘤病因学、进展和结果尚不清楚。 明白为了加速发现MM患者的新疗法，多发性骨髓瘤研究 基金会（MMRF）开发了纵向CoMMpass研究。这项工作由乔纳森·济慈博士领导， TGen已经使用体细胞突变和转录谱鉴定了新的MM亚型。但 基因调控对患者预后的潜在影响的遗传结构尚未被研究。使用 根据CoMMpass数据，我们鉴定了7，737个与基因表达变化相关的变异体（表达 数量性状基因座（eQTL）;其中1，764个是雄性特异性eQTL，847个是雌性特异性eQTL。 此外，在CoMMPass队列中，1，034个鉴定的eQTL与存活相关。然而，在这方面， 功能验证是必要的，以确认监管效果，并更好地评估功能后果 这种变化。为此，我建议使用多重高通量CRISPR激活剂/干扰剂， （CRISPRa/i）筛选，然后进行单细胞RNA测序，以验证推定的顺式调控基因座在 基因表达水平。为了确定这些位点如何调节肿瘤病因，我将进行检测， 这些扰动对肿瘤适应性和对治疗的反应的影响。这项研究将提供 对MM发生、进展和对以下疾病的反应的监管格局的有价值的见解 治疗，并为MM患者开发更有针对性的治疗的潜在候选人。而且 我在这项研究中接受的关于癌症遗传学和癌症基因组学的培训将为以下方面提供新的机会： 我作为独立调查员的未来研究方向

ABSTRACT Multiple Myeloma (MM) is a malignancy of plasma cells and the second most common hematological cancer accounting for 2% of cancer deaths. MM is associated with a poor prognosis, and while new therapies have improved survival rates, most patients still experience relapses. MM shows a strong hereditary genetic component as relatives of MM patients have a two- to four-fold higher risk of disease development. Moreover, MM displays a disparity in occurrence and mortality among sexes with males having a higher risk than females. Many risk loci associated with MM susceptibility identified by genome-wide association studies (GWAS) and meta-analysis are located within or adjacent to the regulatory regions, indicating a role in transcriptional regulation. However, how these risk loci contribute to tumor etiology, progression and outcome are poorly understood. To accelerate the discovery of novel treatments for MM patients, the Multiple Myeloma Research Foundation’s (MMRF) developed the longitudinal CoMMpass study. This work, led by Dr. Jonathan Keats at TGen, has identified novel MM subtypes using somatic mutation and transcription profile. Nevertheless, the genetic architecture underlying gene regulation contributing to patient outcomes has not been examined. Using the CoMMpass data, we identified 7,737 variants associated with changes in gene expression (expression quantitative trait locus; eQTL); among these 1,764 are male-specific and 847 are female-specific eQTLs. Furthermore, 1,034 of the identified eQTLs are associated with survival in the CoMMpass cohort. However, functional validation is necessary to confirm the regulatory effects and better assess the functional consequences of this variation. To this end, I propose using a multiplex high throughput CRISPR activator/interference (CRISPRa/i) screen followed by single-cell RNA sequencing to validate the role of putative cis-regulatory loci on gene expression levels. To determine how these loci modulate tumor etiology, I will perform assays investigating the effects of these perturbations on tumor fitness and response to treatment. The proposed study will provide valuable insights into the regulatory landscape underlying MM occurrence, progression, and response to treatment, and potential candidates for developing more targeted treatments for MM patients. Furthermore, the training I will receive in this study on cancer genetics and cancer genomics will open up new opportunities for my future research directions as an independent investigator.