Moura Ronald, Pontillo Alessandra, D'Adamo Pio, Pirastu Nicola, Campos Coelho Antonio, Crovella Sergio
Department of Genetics, Federal University of Pernambuco, Recife, Brazil;
Department of Immunology, Institute of Biomedical Sciences, University of San Paolo, Brazil.
J Int AIDS Soc. 2014 Jan 10;17(1):18938. doi: 10.7448/IAS.17.1.18938. eCollection 2014.
With the aim of searching genetic factors associated with the response to an immune treatment based on autologous monocyte-derived dendritic cells pulsed with autologous inactivated HIV, we performed exome analysis by screening more than 240,000 putative functional exonic variants in 18 HIV-positive Brazilian patients that underwent the immune treatment.
Exome analysis has been performed using the ILLUMINA Infinium HumanExome BeadChip. zCall algorithm allowed us to recall rare variants. Quality control and SNP-centred analysis were done with GenABEL R package. An in-house implementation of the Wang method permitted gene-centred analysis.
CCR4-NOT transcription complex, subunit 1 (CNOT1) gene (16q21), showed the strongest association with the modification of the response to the therapeutic vaccine (p=0.00075). CNOT1 SNP rs7188697 A/G was significantly associated with DC treatment response. The presence of a G allele indicated poor response to the therapeutic vaccine (p=0.0031; OR=33.00; CI=1.74-624.66), and the SNP behaved in a dominant model (A/A vs. A/G+G/G p=0.0009; OR=107.66; 95% CI=3.85-3013.31), being the A/G genotype present only in weak/transient responders, conferring susceptibility to poor response to the immune treatment.
CNOT1 is known to be involved in the control of mRNA deadenylation and mRNA decay. Moreover, CNOT1 has been recently described as being involved in the regulation of inflammatory processes mediated by tristetraprolin (TTP). The TTP-CCR4-NOT complex (CNOT1 in the CCR4-NOT complex is the binding site for TTP) has been reported as interfering with HIV replication, through post-transcriptional control. Therefore, we can hypothesize that genetic variation occurring in the CNOT1 gene could impair the TTP-CCR4-NOT complex, thus interfering with HIV replication and/or host immune response.
Being aware that our findings are exclusive to the 18 patients studied with a need for replication, and that the genetic variant of CNOT1 gene, localized at intron 3, has no known functional effect, we propose a novel potential candidate locus for the modulation of the response to the immune treatment, and open a discussion on the necessity to consider the host genome as another potential variant to be evaluated when designing an immune therapy study.
为了寻找与基于自体灭活HIV脉冲刺激的自体单核细胞衍生树突状细胞免疫治疗反应相关的遗传因素，我们对18名接受免疫治疗的巴西HIV阳性患者中超过240,000个推定的功能性外显子变异进行了外显子组分析。
使用ILLUMINA Infinium HumanExome BeadChip进行外显子组分析。zCall算法使我们能够召回罕见变异。使用GenABEL R包进行质量控制和以单核苷酸多态性（SNP）为中心的分析。Wang方法的内部实现允许进行以基因为中心的分析。
CCR4-NOT转录复合体亚基1（CNOT1）基因（16q21）与治疗性疫苗反应的改变显示出最强的关联（p = 0.00075）。CNOT1 SNP rs7188697 A/G与树突状细胞（DC）治疗反应显著相关。G等位基因的存在表明对治疗性疫苗反应不佳（p = 0.0031；比值比[OR]=33.00；可信区间[CI]=1.74 - 624.66），并且该SNP呈显性模式（A/A与A/G + G/G相比，p = 0.0009；OR = 107.66；95% CI = 3.85 - 3013.31），A/G基因型仅存在于弱/短暂反应者中，赋予对免疫治疗反应不佳的易感性。
已知CNOT1参与mRNA去腺苷酸化和mRNA降解的控制。此外，最近有报道称CNOT1参与由锌指蛋白36（TTP）介导的炎症过程的调节。据报道，TTP-CCR4-NOT复合体（CCR4-NOT复合体中的CNOT1是TTP的结合位点）通过转录后控制干扰HIV复制。因此，我们可以假设CNOT1基因中发生的遗传变异可能损害TTP-CCR4-NOT复合体，从而干扰HIV复制和/或宿主免疫反应。
鉴于我们的发现仅适用于所研究的18名患者且需要重复验证，并且位于内含子3的CNOT1基因的遗传变异尚无已知的功能效应，我们提出了一个用于调节免疫治疗反应的新的潜在候选基因座，并开启了关于在设计免疫治疗研究时将宿主基因组作为另一个需要评估的潜在变异的必要性的讨论。
