Whole blood gene expression to identify biomarkers of disease risk, progression and response to therapy in Type 1 diabetes

总结 在这项资助中，我们建议对外周血细胞进行基因表达分析 (PBC)T1 D患者的自身抗体阴性一级亲属（AA-FDR）和AA+ 进展（进展者）或未进展为高血糖（非进展者）的FDR 进展者），与健康的非T1 D相关对照相比。我们还将执行基因 入组TrialNet Abatacept（CTLA 4-IG）New的患者PBMC的表达分析 发作研究（TN-09）。拟议的研究将确认和扩展我们在 疾病易感性和疾病进展的全血生物标志物的鉴定 T1 D，并启动我们对治疗反应的生物标志物的研究。 在JDRF资助下产生的初步数据表明，PBC基因 T1 D和T1 D相关个体的表达谱彼此相似，而不是 健康正常的非糖尿病相关对照;即存在前驱基因表达 可以识别T1 D患者的AA-FDR的PBMC中的疾病风险的特征， 疾病的临床症状。基于这些初步数据，我们假设T1 D家族 所有患者都有一个环境驱动的，表观遗传控制的基因表达特征， 在外周血中可以看到。我们发现了一个AA-FDR的子集， 干扰素诱导的PBMC中基因表达水平升高。这些人也 表达的基因表达特征与AA+ FDR更相似， 与未进展的AA+ FDR或其他AA-FDR和对照相比， 这表明全血基因表达生物标志物可用于识别个体， 在血清转化之前会发展为高血糖症。在血清转化的患者中， (AA+），我们发现基因表达在疾病的早期阶段变化最大（>3 在高血糖症发作前10年）的进展者与非进展者相比。这 表明我们可能能够识别生物标志物，不仅区分AA+进展者， 从AA+非进展者，但也预测疾病进展的速度。最后，研究 已经表明PBC基因表达特征在新近发病的高血糖患者中不同， 对抗CD 3治疗有反应的患者与无反应的患者相比（AbATE试验）。我们 假设我们也可以看到对化疗有反应的患者的基因表达差异， CTA 4-IG（阿巴西普）与无应答者相比，开始治疗后3个月， 治疗（TN-09）。如果能及早发现无应答者，这将为其他治疗提供时间。 在β细胞质量/功能完全丧失之前测试疗法。 提出了三个具体目标。第一个具体目标是验证前驱 在糖尿病相关AA-个体中观察到的基因表达模式。第二个具体目标是 为了鉴定T1 D疾病进展的PBC基因表达特征（鉴定那些 谁将进展到T1 D从那些谁不会），和一个进展率的签名。的 第三个具体目标是询问是否存在PBC基因表达特征， 近期发作患者接受CTLA 4-IG干预的应答者与非应答者表型 使用TN 09样品的高血糖患者。本申请中描述的研究需要 来自TrialNet的PBC RNA样本。我们已经从TrialNet收到了超过300个样本 储存库，并已收到临时批准接收额外的样品（信函 附件）。

Summary In this grant, we propose to perform gene expression analysis on peripheral blood cells (PBC) of auto-antibody negative first degree relatives of T1D patients (AA- FDRs) and AA+ FDRs who have either progressed (progressors) or not progressed to hyperglycemia (non- progressors), compared to healthy non-T1D related controls. We will also perform gene expression analysis on PBCs of patients enrolled in the TrialNet Abatacept (CTLA4-Ig) New Onset Study (TN-09). The proposed studies will confirm and extend our work on the identification of whole blood biomarkers of disease susceptibility and disease progression in T1D, and initiate our studies on biomarkers of response to therapy. Preliminary data generated under funding from the JDRF suggests that the PBC gene expression profiles of T1D and T1D-related individuals are more similar to each other than to healthy normal non-diabetes-related controls; that is, there is a prodromal gene expression signature that can identify disease risk in the PBCs of AA- FDRs of T1D patients who show no clinical signs of disease. Based on these preliminary data, we hypothesize that families of T1D patients, all have an environmentally-driven, epigenetically-controlled gene expression signature of risk that can be seen in peripheral blood. We identified a subset of AA- FDRs that had elevated levels of interferon-induced gene expression in their PBCs. These individuals also expressed a gene expression signature that was more similar to AA+ FDRs who progressed to hyperglycemia than to AA+ FDRs who did not progress, or to other AA- FDRs, and to controls, suggesting that whole blood gene expression biomarkers could be used to identify individuals who will progress to hyperglycemia prior to seroconversion. In patients who seroconverted (AA+), we found that gene expression was most changed during the early stages of disease (>3 years before the onset of hyperglycemia) in progressors compared to non-progressors. This indicates that we might be able to identify biomarkers that not only distinguish AA+ progressors from AA+ non-progressors, but also predict the rate of disease progression. Finally, studies have shown that PBC gene expression signatures differ in recent onset hyperglycemic patients that responded to anti-CD3 therapy compared to those who did not respond (AbATE trial). We hypothesize that we may also see a difference in gene expression in patients who respond to CTA4-Ig (Abatacept) compared to those who do not respond, 3 months after the initiation of therapy (TN-09). If non-responders could be identified early, this would allow time for other therapies to be tested before total loss of beta cell mass/function occurs. Three specific aims are proposed. The first specific aim is to validate the prodromal gene expression pattern seen in diabetes related AA- individuals. The second specific aim is to identify both a PBC gene expression signature of T1D disease progression (identifying those who will progress to T1D from those who will not), and a signature of rate of progression. The third specific aim is to ask if there is a PBC gene expression signature that might predict responder vs. non-responder phenotypes for intervention with CTLA4-Ig in recent onset hyperglycemic patients using TN09 samples. The studies described in this application require PBC RNA samples from TrialNet. We have already received >300 samples from the TrialNet repository and have received provisional approval to receive additional samples (letter attached).