Identification of Genetic Factors Associated with Infectious Diseases

与传染病相关的遗传因素的鉴定

• 批准号: 10014339
• 负责人: Cheryl Winkler
• 金额: $ 36.45万
• 依托单位: DIVISION OF BASIC SCIENCES - NCI
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10014339
• 关键词: AFP gene; AIDS-Associated Nephropathy; APOL1 gene; Acquired Immunodeficiency Syndrome; Address; Affect; Africa South of the Sahara; African; African American; Aging; Antiviral Agents; Attenuated; Bile Acids; Bilirubin; CUL5 gene; Cancer Etiology; Cardiovascular Diseases; Cell Cycle; Cell Proliferation; Cell division; Cells; China; Chinese People; Chronic Disease; Chronic Hepatitis B; Cirrhosis; Clinical Management; Code; Collaborations; Communicable Diseases; Cytidine Deaminase; Data Set; Databases; Development; Diagnosis; Differentiation and Growth; Disease; Disease Progression; Early Diagnosis; Environmental Risk Factor; Epidemiology; Epigenetic Process; Etiology; Exposure to; Family; Far East; Gene Expression; Gene Expression Profile; Gene Frequency; Genes; Genetic; Genets; Genotype; Goals; HIV; HIV Infections; HIV-1; Hepatitis B Virus; Hepatitis C; Hepatocyte; High Prevalence; Human; Immunologic Factors; In Vitro; Infection; International; Investigation; Kidney; Kidney Diseases; Lead; Liver; Liver Cirrhosis; Liver Regeneration; Liver diseases; Lysosomes; MKI67 gene; Malignant Neoplasms; Malignant neoplasm of liver; Mentors; Meta-Analysis; Metabolic; Modification; Mutagens; Natural History; Natural Immunity; Normal tissue morphology; Odds Ratio; Opportunistic Infections; Organ; Other Genetics; Outcome; Participant; Pathogenesis; Pathogenicity; Pathway interactions; Patient-Focused Outcomes; Patients; Penetrance; Persons; Pharmacotherapy; Plasma; Population; Predisposition; Premature aging syndrome; Prevention; Primary carcinoma of the liver cells; Process; Prognostic Factor; Prognostic Marker; Proteins; Public Health; RNA; Randomized; Receptor Cell; Reporting; Research; Research Design; Research Personnel; Resistance; Retroelements; Retroviridae; Risk; Risk Factors; Role; Series; Single-Stranded DNA; Somatic Mutation; South Africa; South African; Southern Africa; TGFB1 gene; TP53 gene; Taurocholate Sodium; Testing; The Cancer Genome Atlas; Therapeutic; Tissue Sample; Tissues; Tumor Tissue; UGT1A1 gene; Ultrasonography; Vaccines; Validation; Variant; Viral; Viral Load result; Virus Diseases; Virus Receptors; Virus Replication; Yang; acquired immunity; antiretroviral therapy; carcinogenesis; chronic infection; cohort; cytotoxic; differential expression; disorder risk; follow-up; genetic variant; genome wide association study; global health; insight; lipid disorder; liver inflammation; macrophage; malignant breast neoplasm; microvesicles; non-alcoholic fatty liver disease; outcome forecast; pandemic disease; polypeptide; predict clinical outcome; prognostic signature; prognostic value; protective effect; protein expression; receptor; receptor function; risk variant; targeted treatment; tool; transcriptomics; transmission process; tumor; viral resistance

Our focus is on two major infectious diseases have enormous impact on global health. HIV-1 is pandemic and HBV infection and HBV-related hepatocellular carcinoma (HCC) is prevalent in East Asia and sub-Saharan Africa, globally affecting millions of people. Our objective is to identify genetic factors that contribute to the occurrence and development of theseinfectious diseases. The identification of host proteins involved in viral replication, in innate or acquired immunity, or in carcinogenesis pathways will provide critical insights for the rational development of antiviral drugs and effective vaccines. Our strategy is to identify genetic variants that differentially affect rates of infection, or the course of pathogenesis, and which thereby identify the variant-containing gene using targeted gene, genome wide association study (GWAS), and functional approaches. We have formed international collaborations with researchers in South Africa and China to mentor fellows, build capacity, and perform research that address important public health questions (i.e. HIV in South Africa and HBV-associated liver cancer in China. Accomplishments in HIV disease: 1) APOL1 renal risk variants interact strongly with HIV to cause HIV-associated nephropathy with odds ratios ranging from 29 in African Americans to 89 in southern Africa. In vitro studies suggest that APOL1, an innate immune factor, impedes HIV replication by several mechanisms, including a pathway involving secretion of Vif in microvesicles and degradation of Vif in lysosomes. We hypothesized that APOL1 coding variants might attenuate the protective effect of ancestral APOL1 resulting in higher viral burden or increased transmission of HIV. This could possibly contribute to the high burden of HIV disease in sub-Saharan African were APOL1 risk variants are very common, with allele frequencies ranging from 10-50%. We therefore conducted genetic epidemiological association analyses of HIV patients with longitudinal follow-up spanning the pre- and post-antiretroviral treatment eras. We found that the variants do not increase the risk of HIV-1 infection and are not associated with viral load or progression to AIDS. This finding suggests that APOL1 variants do not contribute to the higher prevalence of HIV infections in sub-Saharan Africa or in African Americans (An et al. Front Immunol, 2019). 2) Because APOL1 variants also dysregulate macrophage differentiation, we have explored its role in the development of optimistic infections in persons with HIV infection. Our findings suggest that APOL1 variants may confer protection specifically against fungal opportunistic infections. We are now replicating this finding in independent HIV natural history cohorts. Accomplishments in HBV-associated liver cancer: 1) Genetic variants in the HBV receptor NTCP ( modify risk to HBV infection and progression to liver cirrhosis. Sodium taurocholate co-transporting polypeptide (NTCP/SLC10A1) was recently identified as a cell receptor for HBV cell entry. The S267F variant causes the loss of the HBV receptor function. We assessed the association of NTCP/SLC10A1 S267F in over 1000 patients with distinct HBV infection outcomes: HBV resistance, clearance, chronic infection, cirrhosis, and HCC. The NTCP/SLC10A1 S267F coding variant was associated with increased resistance to HBV infection and decreased risk of development of cirrhosis, but not with modified risk of HCC (An et al. JID 2018), validating the etiological role of the NTCP/SLC10A1 receptor as a primary HBV receptor. NTCP/SLC10A1 antigonists might provide therapeutic benefit in patients with chronic HBV infection by decreasing progression to liver cirrhosis. We are also investigating the expression and prognostic value of NTCP/SLC10A1 in HCC tumor-normal tissue pairs by integrating and meta-analyzing eight gene expression datasets (n=1200) derived from GEO and TCGA data sets. The expression level of NTCP/SLC10A1 was markedly decreased in HCC tumor tissues compared with corresponding normal tissues in multiple datasets and the low expression was associated with poor survival. We are in the process of detecting NTCP/SLC10A1 protein expression levels in HCC tissues. We postulate that decreased NTCP/SLC10A1 may lead to over-accumulation of bile acids, which is potentially cytotoxic to hepatocytes, causing liver inflammation and regeneration. 2) Mildly elevated bilirubin levels are reported to be associated with decreased risk of non-alcoholic fatty liver disease (NAFLD), a risk factor for HCC; however, the direction of causality is unknow. In a collaborative study with colleagues in China, we tested the hypothesis that genetically elevated plasma bilirubin levels are causally related to reduced risk of NAFLD in 403 participants with liver ultrasonography. NAFLD was diagnosed in 19% of study participants. Two variant alleles in UGT1A1 10-12% of the variance in bilirubin levels. In a multivariant analysis using a Mendelian randomization approach, we found that UGT1A1 genotypes did not associated with NAFLD. We also found that plasma bilirubin levels were not associated with risk of NAFLD. These two results suggest that bilirubin is unlikely to be causally related to NAFLD risk (Luo et al, Front Genet, 2018). 3) Our group also contributed to a series of studies by our Chinese colleagues to identify prognostic biomarkers for HCC prognosis by providing assistance with study design and analysis. Ki-67 (MKI67) is a gene that regulates cell proliferation, differentiation, and growth. Through public database analyses, we found that MKI67 expression level was associated with TGFB1 expression in liver cancer tissues and higher MKI67 expression level was associated with poorer survival in patients with HBV-related HCC, suggesting that MK167 expression levels may predict clinical outcomes of patients with HBV-related HCC (Yang et al. Cancer Manag Res, 2018). A second study was to identify competing endogenous RNA (ceRNA) network using dysregulated RNAs between tumor and adjacent liver tissues in the Cancer Genome Atlas (TCGA) and to investigate underlying prognostic factors in HCC patients. This study constructed a ceRNA network and gene set enriched in pathways of the cell cycle, cell division, and cell proliferation. The prognostic signature may provide an independent tool for prediction of HCC survival (Liao et al., J Cancer, 2019). 4) There is lack of validations across limited transcriptomic studies in HBV-related HCC. We performed a meta-analysis to assess changes in gene expression patterns by integrating HBV-HCC samples from TCGA and GEO datasets. Our analysis revealed that over 500 differentially expressed genes (DEG) were shared across all datasets, indicating that approximately 8% of differentially expressed genes from TCGA HBV-HCC are replicated across studies. The identified pathways and genes may be useful for development of targeted therapies and prevention once validated, as we are doing in our South African cohort of HBV-associated HCC. 5) Cytidine deaminases of the human APOBEC3 family (encoded by the APOBEC3 A-H genes) restrict retroviruses and mobile retroelements but they can also hypermutate host single strand (ss)DNA. We previously identified several genetic variants in the A3G, A3B, A3F and CUL5 of A3-VIf pathway that affect HIV-1 infection or progression. A3B/A3A have been recently recognized as strong endogenous mutagens in multiple cancers. The A3B deletion has been associated with elevated risk to breast cancer. We found that a functional SNP affecting APOBEC3A/B expression was associated with AFP levels in HCC patients, implicating APOBEC3 role in HCC development. We are now extending our investigation to the interaction of APOBEC3B deletion and HCC hot somatic mutations of TP53 and TERT.

我们的重点是对全球健康产生巨大影响的两种主要传染病。 HIV-1 呈流行病，HBV 感染和 HBV 相关肝细胞癌 (HCC) 在东亚和撒哈拉以南非洲地区普遍存在，影响全球数百万人。我们的目标是确定导致这些传染病发生和发展的遗传因素。鉴定参与病毒复制、先天或获得性免疫或致癌途径的宿主蛋白将为合理开发抗病毒药物和有效疫苗提供重要见解。我们的策略是识别对感染率或发病过程有不同影响的遗传变异，从而利用目标基因、全基因组关联研究 (GWAS) 和功能方法识别包含变异的基因。我们与南非和中国的研究人员建立了国际合作，以指导研究员、建设能力并开展研究，以解决重要的公共卫生问题（即南非的艾滋病毒和中国的乙型肝炎相关肝癌。艾滋病毒疾病方面的成就：1） APOL1 肾脏风险变异与 HIV 强烈相互作用，导致 HIV 相关肾病，其比值比范围从非裔美国人的 29 到南部非洲的 89。体外研究表明，APOL1（一种先天免疫因子）通过多种机制阻碍 HIV 复制，包括涉及微泡中 Vif 分泌和溶酶体中 Vif 降解的途径。我们假设 APOL1 编码变异可能会削弱祖先 APOL1 的保护作用，导致更高的病毒负荷或增加 HIV 的传播。这可能会导致撒哈拉以南非洲地区艾滋病毒疾病的高负担，因为 APOL1 风险变异非常常见，等位基因频率范围为 10-50%。因此，我们对艾滋病毒患者进行了遗传流行病学关联分析，并在抗逆转录病毒治疗前后进行了纵向随访。我们发现这些变异不会增加 HIV-1 感染的风险，并且与病毒载量或艾滋病进展无关。这一发现表明，APOL1 变异不会导致撒哈拉以南非洲地区或非裔美国人的艾滋病毒感染率较高（An et al. Front Immunol, 2019）。 2) 由于 APOL1 变异也会调节巨噬细胞分化，因此我们探讨了其在 HIV 感染者乐观感染发展中的作用。我们的研究结果表明，APOL1 变异体可能具有专门针对真菌机会性感染的保护作用。我们现在正在独立的艾滋病毒自然史队列中复制这一发现。在HBV相关肝癌方面的成就：1）HBV受体NTCP的基因变异（改变HBV感染和进展为肝硬化的风险。牛磺胆酸钠共转运多肽（NTCP/SLC10A1）最近被鉴定为HBV细胞的细胞受体S267F 变异导致 HBV 受体功能丧失，我们评估了 NTCP/SLC10A1 S267F 的关联。 1000 名具有不同 HBV 感染结果的患者：HBV 耐药、清除、慢性感染、肝硬化和 HCC NTCP/SLC10A1 S267F 编码变异与 HBV 感染耐药性增加和肝硬化发生风险降低相关，但与肝硬化风险改变无关。 HCC（An et al. JID 2018），验证了 NTCP/SLC10A1 受体作为主要 HBV 受体的病因学作用。 NTCP/SLC10A1 拮抗剂可能通过减少肝硬化进展为慢性 HBV 感染患者提供治疗益处。我们还通过整合和荟萃分析八个基因表达来研究 NTCP/SLC10A1 在 HCC 肿瘤-正常组织对中的表达和预后价值。来自 GEO 和 TCGA 数据集的数据集 (n=1200)。在多个数据集中，与相应的正常组织相比，NTCP/SLC10A1在HCC肿瘤组织中的表达水平显着降低，并且低表达与较差的生存率相关。我们正在检测 HCC 组织中 NTCP/SLC10A1 蛋白的表达水平。我们假设 NTCP/SLC10A1 减少可能导致胆汁酸过度积累，这对肝细胞具有潜在的细胞毒性，导致肝脏炎症和再生。 2) 据报道，胆红素水平轻度升高与非酒精性脂肪性肝病 (NAFLD) 风险降低相关，NAFLD 是 HCC 的危险因素；然而，因果关系的方向是未知的。在与中国同事的一项合作研究中，我们对 403 名接受肝脏超声检查的参与者进行了检验，测试了这样的假设：血浆胆红素水平升高与 NAFLD 风险降低存在因果关系。 19% 的研究参与者被诊断出 NAFLD。 UGT1A1 中的两个变异等位基因使胆红素水平存在 10-12% 的变异。在使用孟德尔随机化方法的多变量分析中，我们发现 UGT1A1 基因型与 NAFLD 无关。我们还发现血浆胆红素水平与 NAFLD 风险无关。这两个结果表明胆红素不太可能与 NAFLD 风险存在因果关系（Luo 等人，Front Genet，2018）。 3) 我们小组还为中国同事的一系列研究做出了贡献，通过提供研究设计和分析方面的帮助来确定 HCC 预后的生物标志物。 Ki-67 (MKI67) 是一种调节细胞增殖、分化和生长的基因。通过公共数据库分析，我们发现肝癌组织中 MKI67 表达水平与 TGFB1 表达相关，并且较高的 MKI67 表达水平与 HBV 相关 HCC 患者较差的生存率相关，这表明 MK167 表达水平可以预测肝癌患者的临床结果。 HBV 相关 HCC（Yang 等人 Cancer Manag Res，2018）。第二项研究是利用癌症基因组图谱 (TCGA) 中肿瘤和邻近肝组织之间失调的 RNA 来识别竞争性内源性 RNA (ceRNA) 网络，并研究 HCC 患者的潜在预后因素。本研究构建了富含细胞周期、细胞分裂和细胞增殖途径的 ceRNA 网络和基因集。预后特征可能为预测 HCC 生存提供独立工具（Liao 等人，J Cancer，2019）。 4) HBV 相关 HCC 的转录组学研究有限，缺乏验证。我们通过整合 TCGA 和 GEO 数据集中的 HBV-HCC 样本进行荟萃分析，以评估基因表达模式的变化。我们的分析显示，所有数据集中共有超过 500 个差异表达基因 (DEG)，这表明 TCGA HBV-HCC 中大约 8% 的差异表达基因在各个研究中重复。正如我们在南非 HBV 相关 HCC 队列中所做的那样，所确定的途径和基因一旦得到验证，可能有助于开发靶向治疗和预防。 5) 人类 APOBEC3 家族的胞苷脱氨酶（由 APOBEC3 A-H 基因编码）限制逆转录病毒和移动逆转录因子，但它们也可以使宿主单链 (ss)DNA 发生超突变。我们之前在 A3-VIf 通路的 A3G、A3B、A3F 和 CUL5 中发现了几个影响 HIV-1 感染或进展的遗传变异。 A3B/A3A 最近被认为是多种癌症中强内源性诱变剂。 A3B 缺失与乳腺癌风险升高有关。我们发现影响 APOBEC3A/B 表达的功能性 SNP 与 HCC 患者的 AFP 水平相关，这表明 APOBEC3 在 HCC 发展中的作用。我们现在正在将研究扩展到 APOBEC3B 缺失与 HCC TP53 和 TERT 热体细胞突变之间的相互作用。