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卫生产生巨大影响的两种主要传染病。艾滋病毒-1是大流行，HBV感染和HBV相关的肝细胞癌（HCC）在东亚和撒哈拉以南非洲普遍存在，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、先天免疫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。我们的策略是识别不同影响感染率或发病过程的遗传变异，从而使用靶基因、基因组全关联研究（GWAS）和功能方法识别含有变异的基因。我们与南非和中国的研究人员建立了国际合作关系，以指导研究员，建立能力，并开展研究，解决重要的公共卫生问题（即南非的艾滋病毒和中国的hbv相关肝癌）。在HIV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，比值比从非洲裔美国人的29到南部非洲的89不等。体外研究表明，先天免疫因子APOL1通过多种机制阻碍HIV复制，包括微囊泡中Vif的分泌和溶酶体中Vif的降解途径。我们假设APOL1编码变异体可能减弱祖先APOL1的保护作用，导致更高的病毒负担或增加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，等位基因频率在10-50%之间。因此，我们对抗逆转录病毒治疗前后的HIV患者进行了遗传流行病学关联分析。我们发现这些变异不会增加HIV-1感染的风险，也与病毒载量或艾滋病的进展无关。这一发现表明，APOL1变异与撒哈拉以南非洲或非洲裔美国人较高的艾滋病毒感染率无关（An等）。Front immuno1, 2019)。2)由于APOL1变异也会失调巨噬细胞分化，我们已经探索了它在HIV感染者乐观感染发展中的作用。我们的研究结果表明，APOL1变异可能对真菌机会性感染具有特异性保护作用。我们现在正在独立的HIV自然史队列中复制这一发现。HBV相关肝癌的研究成果：1)HBV受体NTCP的遗传变异（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）最近被确定为HBV进入细胞的细胞受体。S267F变异导致HBV受体功能丧失。我们评估了NTCP/SLC10A1 S267F在1000多例不同HBV感染结局患者中的相关性：HBV抵抗、清除、慢性感染、肝硬化和HCC。NTCP/SLC10A1 S267F编码变体与HBV感染抵抗力增强和肝硬化发展风险降低相关，但与HCC风险改变无关（An等）。JID 2018)，验证了NTCP/SLC10A1受体作为原发性HBV受体的病因学作用。NTCP/SLC10A1抗菌剂可能通过减少慢性HBV感染患者的肝硬化进展而提供治疗益处。我们还通过整合和meta分析来自GEO和TCGA数据集的8个基因表达数据集（n=1200），研究了NTCP/SLC10A1在HCC肿瘤-正常组织对中的表达和预后价值。在多个数据集中，NTCP/SLC10A1在HCC肿瘤组织中的表达水平明显低于相应的正常组织，低表达与生存率低相关。我们正在检测NTCP/SLC10A1蛋白在HCC组织中的表达水平。我们推测NTCP/SLC10A1的降低可能导致胆汁酸的过度积累，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的一个危险因素；然而，因果关系的方向是未知的。在一项与中国同事的合作研究中，我们对403名接受肝脏超声检查的参与者进行了假设，即遗传性血浆胆红素水平升高与NAFLD风险降低有因果关系。19%的研究参与者被诊断为NAFLD。UGT1A1的两个变异等位基因占胆红素水平变异的10-12%。在使用孟德尔随机化方法的多变异分析中，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的风险无关。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 et al, Front Genet, 2018）。3)我们小组还参与了我们中国同事的一系列研究，通过协助研究设计和分析来确定HCC预后的预后生物标志物。Ki-67 （MKI67）是一种调节细胞增殖、分化和生长的基因。通过公开数据库分析，我们发现肝癌组织中MKI67表达水平与TGFB1表达相关，MKI67表达水平越高，hbv相关HCC患者的生存期越差，提示MK167表达水平可以预测hbv相关HCC患者的临床结局（Yang等）。癌症管理，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的失调RNA来识别竞争内源性RNA （ceRNA）网络，并研究HCC患者的潜在预后因素。本研究构建了一个丰富细胞周期、细胞分裂和细胞增殖通路的ceRNA网络和基因集。预后特征可能是预测HCC生存的独立工具（Liao et al., J Cancer, 2019）。4)在有限的hbv相关HCC转录组学研究中缺乏验证。我们进行了一项荟萃分析，通过整合来自TCGA和GEO数据集的HBV-HCC样本来评估基因表达模式的变化。我们的分析显示，超过500个差异表达基因（DEG）在所有数据集中共享，表明大约8%的TCGA HBV-HCC差异表达基因在研究中被复制。正如我们在南非hbv相关HCC队列中所做的那样，一旦得到验证，已确定的途径和基因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）限制逆转录病毒和可移动的逆转录元件，但它们也可以使宿主单链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的强内源性诱变剂。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AFP水平相关，暗示APOBEC3在HCC发展中的作用。我们现在正在将我们的研究扩展到APOBEC3B缺失与肝癌TP53和TERT的热体细胞突变的相互作用。