MOESM2 of The role of antigen presenting cells in the induction of HIV-1 latency in resting CD4+ T-cells

Additional file 2: Table S1. Comparison of gene expression between latency inducing and non-inducing antigen presenting cell subpopulations using RNA-seq. Using the bioinformatics databases DAVID [80], GeneCards and GeneCodis, cell compartment gene function was determine of each gene. Genes expressed on antigen presenting cell (APC)-surface with the ability to signal to T-cells were shortlisted and their role in HIV-1 infection and DC-T-cell interaction was further determined using PubMed. Genes that were common to the RNA-seq and microarray generated gene lists are in italics and underlined in Table 1. Acronyms used: intracellular adhesion molecules (ICAM), C-type lectin (CLEC), immunoglobulin (Ig), T-cell immune-receptor with Ig and tyrosine-based inhibition motif (ITIM) domains (TIGIT), DNAX accessory molecule-1 (DNAM-1), cytotoxic and regulatory T-cell molecule (CRTAM), junction adhesion molecules (JAMs), blood brain barrier (BBB), leukocyte function antigen (LFA), dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin (DC-SIGN), galectin-1 (Gal-1), cysteine-dependent aspartate-directed proteases (caspase), factor for adipocyte differentiation 158 (FAD158), extracellular matrix (ECM), lymph node (LN), nuclear factor-kappa-B (NFkB), vascular endothelial growth factor (VEGF), major histocompatibility complex (MHC), T-cell receptor (TcR), cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), TYRO protein tyrosine kinase-binding protein (TYROBP), interleukin (IL-), nuclear factor of activated T-cells (NFAT), vasoactive intestinal polypeptide receptor 1 (VIPR1), T-cell immunoglobulin mucin-3 (Tim-3), monocyte derived dendritic cells (MDDC), natural killer cells (NK), human T-lymphotropic virus (HTLV-1), NFAT activating protein with immune-receptor tyrosine-based activation motif (NFAM1, CNAIP), cortical thymocyte-like protein (CTH, CTXC), B-cell receptor (BcR), HIV-associated neurocognitive disorder (HAND), antibody dependent cellular cytotoxicity (ADCC), Fc receptor (FcR), scavenger receptor class-A-1 (SRA-1), epidermal growth factor like domain, multiple/protein 5/9 (EGFL5).

附加文件2：表S1。本研究通过RNA测序（RNA-seq）对比了潜伏期诱导型与非诱导型抗原呈递细胞亚群间的基因表达差异。借助DAVID[80]、GeneCards及GeneCodis生物信息学数据库，对各基因的细胞区室基因功能进行注释。随后筛选出在抗原呈递细胞（antigen presenting cell, APC）表面表达且可向T细胞传递信号的基因，并通过PubMed进一步探究这些基因在HIV-1感染及树突状细胞-T细胞互作中的作用。RNA测序与微阵列分析得到的共有基因在表1中以斜体加下划线标注。所用缩略语如下：细胞间黏附分子（intracellular adhesion molecules, ICAM）、C型凝集素（C-type lectin, CLEC）、免疫球蛋白（immunoglobulin, Ig）、含免疫球蛋白及基于酪氨酸的抑制基序结构域的T细胞免疫受体（T-cell immune-receptor with Ig and tyrosine-based inhibition motif domains, TIGIT）、DNAX辅助分子-1（DNAX accessory molecule-1, DNAM-1）、细胞毒性与调节性T细胞分子（cytotoxic and regulatory T-cell molecule, CRTAM）、连接黏附分子（junction adhesion molecules, JAMs）、血脑屏障（blood brain barrier, BBB）、白细胞功能抗原（leukocyte function antigen, LFA）、树突状细胞特异性细胞间黏附分子-3结合非整合素（dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin, DC-SIGN）、半乳糖凝集素-1（galectin-1, Gal-1）、半胱天冬氨酸蛋白酶（cysteine-dependent aspartate-directed proteases, caspase）、脂肪细胞分化因子158（factor for adipocyte differentiation 158, FAD158）、细胞外基质（extracellular matrix, ECM）、淋巴结（lymph node, LN）、核因子-κB（nuclear factor-kappa-B, NFkB）、血管内皮生长因子（vascular endothelial growth factor, VEGF）、主要组织相容性复合体（major histocompatibility complex, MHC）、T细胞受体（T-cell receptor, TcR）、细胞毒性T淋巴细胞相关蛋白4（cytotoxic T-lymphocyte-associated protein 4, CTLA-4）、TYRO蛋白酪氨酸激酶结合蛋白（TYRO protein tyrosine kinase-binding protein, TYROBP）、白细胞介素（interleukin, IL-）、活化T细胞核因子（nuclear factor of activated T-cells, NFAT）、血管活性肠肽受体1（vasoactive intestinal polypeptide receptor 1, VIPR1）、T细胞免疫球蛋白黏蛋白分子-3（T-cell immunoglobulin mucin-3, Tim-3）、单核细胞衍生树突状细胞（monocyte derived dendritic cells, MDDC）、自然杀伤细胞（natural killer cells, NK）、人类T淋巴细胞病毒1型（human T-lymphotropic virus, HTLV-1）、含免疫受体酪氨酸活化基序的NFAT活化蛋白（NFAT activating protein with immune-receptor tyrosine-based activation motif, NFAM1, CNAIP）、皮质胸腺细胞样蛋白（cortical thymocyte-like protein, CTH, CTXC）、B细胞受体（B-cell receptor, BcR）、HIV相关神经认知障碍（HIV-associated neurocognitive disorder, HAND）、抗体依赖性细胞介导的细胞毒性（antibody dependent cellular cytotoxicity, ADCC）、Fc受体（Fc receptor, FcR）、清道夫受体A类1（scavenger receptor class-A-1, SRA-1）、表皮生长因子样结构域多蛋白5/9（epidermal growth factor like domain, multiple/protein 5/9, EGFL5）。