Bystander gene deletions in cancer: mechanisms of therapeutic opportunities and challenges

摘要：靶向癌症治疗的一个现状是，在癌症中发现的数千种躯体改变中， 只有癌基因和肿瘤抑制基因等驱动基因的变化才能决定治疗策略。例如, 驱动肿瘤抑制基因PTEN缺失/突变导致AKT和mTOR升高的癌症 信号通路被认为是PI3K/AKT/mTOR抑制剂治疗的合理候选者。因此，PI3K/mTOR 抑制剂已被批准或正在进行临床试验，用于治疗PTEN/PI3K改变的各种癌症。然而，在胶质母细胞瘤中 (GBM)当超过60%的患者出现PTEN功能丧失时，PI3K/AKT/mTOR抑制剂在很大程度上 效果不佳。人们经常忽视的是，当肿瘤抑制基因发生缺失时，附近的基因也会发生 无意中的共同删除。这些旁观者基因不一定是肿瘤抑制基因。事实上，他们中的许多人 对细胞的生长和存活很重要。在某些情况下，这种旁观者缺失事件会产生独特的药物敏感性 尤其是在癌细胞中。例如，POLR2(RNA聚合酶II的一个亚单位)两个等位基因之一的缺失 作为P53缺失的旁观者)减少了POLR2蛋白的数量，并创造了这些细胞对 低剂量的POLR2抑制剂。在癌症中还有其他几个这样的旁观者缺失事件会导致易感性 具体到癌细胞(例如，由于染色体7q22丢失而导致的PSMC2缺失、由于1p36丢失而导致的烯醇化酶1缺失 肿瘤抑制基因、作为染色体1p丢失一部分的MAGOHB缺失以及与肿瘤的MTAP共缺失 抑制子CDKN2A)。通过对TCGA数据库的检索，我们发现了一个重要的致脂基因是半合子 在胶质母细胞瘤、黑色素瘤和前列腺癌中，作为肿瘤抑制基因PTEN(位于10号染色体)的旁观者被删除。 由造脂酶合成的脂肪酸也存在于我们的饮食中。因此，当我们减少这种脂肪酸时 在饮食中，用特定的抑制剂抑制生脂基因的残留活性可杀死胶质母细胞瘤和黑色素瘤 细胞。这个子集(子集1)最终通过应激反应途径获得抗药性，并被 一种特定的应激反应途径的临床前级别的抑制剂。在我们的分析中，我们还意外地发现，这 生脂基因在第二个GBM亚集(亚集2)中由于缺失和结合而完全抑制 甲基化。亚组2失去了一个对生长和增殖至关重要的基因，但却在未知的情况下茁壮成长 替代机制。由于目标致脂基因的缺失，亚群2品系对致脂基因完全抗性 酶抑制剂。研究亚组2GBM的存活机制不在本申请的范围内。 在这项建议中，我们将使用初级GBM株系和测试是否缺失和甲基化状态的脂肪生成 基因可用作抑制剂治疗的生物标记物，与定制的药物饮食相结合。其次，我们将 进行分子、药代动力学/药效学和临床前研究，以解决获得性脑出血的机制 子集1GBM的抗性。这些测试将在建立良好的临床前颅内小鼠模型上进行。 神经胶质瘤。

ABSTRACT: A status-quo in targeted cancer therapy is that out of the thousands of somatic alterations found in cancer, alterations only in driver genes like oncogenes and tumor suppressors determine therapeutic strategy. For example, cancers with deletion/mutation of the driver tumor suppressor gene PTEN and consequently elevated AKT and mTOR signaling are considered rational candidates for PI3K/AKT/mTOR inhibitor therapy. Accordingly, PI3K/mTOR inhibitors are approved or in clinical trials for various cancers with PTEN/PI3K alterations. However, in glioblastoma (GBM) where PTEN loss of function occurs in over 60% of patients, PI3K/AKT/mTOR inhibitors have been largely ineffective. It is often overlooked that when tumor suppressor genes undergo deletion, nearby genes also undergo inadvertent co-deletion. These bystander genes are not necessarily tumor suppressor genes. In fact, many of them are important for cell growth and survival. In some cases, such bystander deletion events create a unique drug sensitivity specifically in cancer cells. For example, deletion of one of the two alleles of POLR2 (a subunit of RNA polymerase II co- deleted as a bystander to P53 deletion) reduces the amount of POLR2 protein and creates high sensitivity of these cells to low dose POLR2 inhibitors. There are several other such bystander deletion events in cancer that causes vulnerability specifically to cancer cells (e.g., PSMC2 deletion due to chromosome 7q22 loss, Enolase 1 deletion due to loss of 1p36 tumor suppressor locus, MAGOHB deletion as part of chromosome 1p loss, and MTAP co-deletion with the tumor suppressor CDKN2A). Searching the TCGA database we have identified that a crucial lipogenic gene is hemizygously deleted as bystander to the tumor suppressor PTEN (on chromosome 10) in glioblastoma, melanoma and prostate cancer. The fatty acid synthesized by the lipogenic enzyme is also present in our diet. Therefore, when we reduced this fatty acid from diet, inhibition of residual activity of the lipogenic gene with specific inhibitors killed glioblastoma and melanoma cells. This subset (subset 1) ultimately acquired drug resistance through a stress response pathway, and were eliminated by a specific pre-clinical grade inhibitor of the stress pathway. During our analysis, we also surprisingly discovered that this lipogenic gene in completely suppressed in a second GBM subset (subset 2) due to a combination of deletion and methylation. Subset 2 lost a gene that is important for growth and proliferation, and yet thrived, through yet unknown alternative mechanisms. Due to loss of the target lipogenic gene, subset 2 lines were completely resistant to the lipogenic enzyme inhibitor. Investigating the mechanism of survival of subset 2 GBM is outside the scope of this application. In this proposal we will use a repertoire of primary GBM lines and test if deletion and methylation status of the lipogenic gene can be used as biomarkers for inhibitor therapy in combination with a custom medicinal diet. Secondly, we will perform molecular, pharmacokinetic/pharmacodynamic and preclinical studies to address the mechanism of acquired resistance of subset 1 GBM. These tests will be performed in a well-established preclinical mouse model of intracranial glioma.