Pathogenesis of the cART unresponsive Kaposi’s sarcoma tumor niche

摘要 卡波西肉瘤（KS）是最常见的艾滋病定义癌症。联合抗逆转录病毒疗法（cART） 大大降低了艾滋病患者中KS相关的死亡率;然而，存在严重的临床问题， 在美国，高达50%的HIV+KS+患者和61%的撒哈拉以南非洲患者从未达到完整的治疗。 甚至在化疗和HIV病毒载量减少的情况下缓解。没有明确的研究表明， 肿瘤相关特征或机制是否与cART进展性KS（进展者）相关， 应答者（responsers）表型。我们的研究利用了来自美国的强大的pre-cART KS组织收集（n = 224）。 ACSR源自卡波西肉瘤抗逆转录病毒药物（ARKS）临床试验。36%的ARKS 参与者经历了持续的KS进展，尽管病毒载量减少， 计数，与1年内肿瘤减少或消除的其他队列相比， 试验终点。本申请提出了关于进展者表型的几个假设：1）在治疗前， 在cART启动后，HIV和/或KSHV感染的免疫细胞的增加增强了刺激性免疫应答。 2）在进行者表型中，KSHV裂解和 免疫调节基因，刺激增加免疫细胞募集到pre-cART肿瘤中 微环境和促进肿瘤进展，通过增强炎症过程中的精氨酸信号 部分通过cART-恢复的免疫系统，3）KS肿瘤的高度炎性性质，包括 与之相互作用的免疫细胞的复杂混合物，选择独特的和/或难以捉摸的HIV基因型， 来自血浆HIV，其促进刺激过程在进展表型中继续。我们的具体 目的是通过结合先进的免疫组织化学、病毒特异性细胞免疫学和细胞免疫学技术来解决这些假设。 定位（DNA和RNAscope），高通量基因表达分析（RNAseq），和一种新的深度 测序方法应用于艾滋病毒。创新包括前所未有的数量pre-cART KS肿瘤 可用于研究的材料，先进的成像技术，体内KS肿瘤基因表达研究， 使用新的PacBio SMRT测序方法应用于艾滋病毒，以及机器学习方法， 可以在复杂的数据集中定义非线性关联。该项目将定义最大的特征鲜明的 一组与cART相关KS结局相关的组合特征，直接来源于KS相关 生物材料在肿瘤小生境pre-cART中鉴定临床相关免疫因子将为肿瘤小生境的免疫治疗铺平道路。 发展未来的机制研究的功能，病毒和细胞基因，参与 cART耐药肿瘤进展。

Abstract Kaposi's Sarcoma (KS) is the most common AIDS-defining cancer. Combined anti-retroviral therapy (cART) has greatly reduced KS-associated mortality among AIDS patients; however, a serous clinical problem exists in that up to 50% of HIV+KS+ patients in the United States and 61% in Sub-Saharan Africa never achieve complete remission even with chemotherapy and a reduction in HIV viral loads. No definitive study has identified if there are tumor-associated features or mechanisms are associated with cART-progressive KS (progressors) vs. the responder (responders) phenotype. Our study utilizes a robust pre-cART KS tissue collection (n = 224) from the ACSR that originated from the Antiretrovirals for Kaposi's Sarcoma (ARKS) clinical trial. 36% of ARKS participants experienced continued progression of KS despite a reduction in viral loads and restored T-cell counts, in contrast to the rest of the cohort who experienced a reduction or elimination of tumors by the 1-year trial endpoint. This application poses several hypotheses concerning the progressor phenotype: 1) prior to the initiation of cART, an increase in HIV and/or KSHV-infected immune cells enhances a stimulatory immunological profile in the progressor phenotype, 2) there are significant differences in the upregulation of KSHV lytic and immunomodulation genes, which stimulate increased immune cell recruitment into the pre-cART tumor microenvironment and promote tumor progression through cytokine-signaling inflammatory processes enhanced in part by the cART-revitalized immune system, 3) the highly inflammatory nature of KS tumors, comprising a complex mixture of immune cells with which to interact, selects for unique and/or elusive HIV genotypes, distinct from plasma HIV, that promote stimulatory processes to continue in the progressor phenotype. Our Specific Aims address these hypotheses using a combination of advanced immunohistochemistry, virus specific cellular localization (DNA and RNAscope), high-throughput gene expression analysis (RNAseq), and a novel deep sequencing approach applied to HIV. Innovations include the unprecedented amount pre-cART KS tumor material available for the study, advanced imagining technologies, in vivo KS tumors gene expression studies, the use of the newer PacBio SMRT sequencing approach applied to HIV, and machine-learning approaches that can define non-linear associations in complex data sets. This project will define the largest well-characterized set of combinatorial features related to cART-associated KS outcomes derived directly from KS-associated biomaterial. Identifying clinically relevant immune factors in the tumor niche pre-cART will pave the way for the development of future mechanistic studies on the functions of both viral and cellular genes that are involved in cART resistant tumor progression.