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: 10262058
• 负责人: Cheryl Winkler
• 金额: $ 31.22万
• 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/10262058
• 关键词: 3' Untranslated Regions; AIDS-Associated Nephropathy; AIDS/HIV problem; APOL1 gene; Acquired Immunodeficiency Syndrome; Acute Renal Failure with Renal Papillary Necrosis; Address; Affect; Africa South of the Sahara; African; African American; Aging; Antiviral Agents; Asians; Attenuated; Biopsy; COVID-19; CUL5 gene; Cancer Etiology; Cardiovascular Diseases; Categories; Cell Cycle; Cell Proliferation; Cell division; China; Chronic Disease; Chronic Hepatitis B; Cirrhosis; Clinical Management; Code; Collaborations; Communicable Diseases; Cytidine Deaminase; DNA; Data Set; Detection; Development; Diagnosis; Dialysis procedure; Disease; Disease Progression; Early Diagnosis; Environmental Risk Factor; Enzymes; Epidemiology; Epigenetic Process; Etiology; Exposure to; Family; Far East; Gene Expression Profile; Gene Frequency; Genes; Genetic; Genetic Variation; Genotype; Goals; HIV; HIV Infections; HIV-1; Haplotypes; Hepatitis B Virus; Hepatitis C; High Prevalence; Human; Immunologic Factors; In Vitro; Individual; Infection; International; Kidney; Kidney Diseases; Lead; Link; Lipids; Liver; Liver diseases; Malignant Neoplasms; Malignant neoplasm of liver; Meta-Analysis; Metabolic; Methods; MicroRNAs; Modification; Mutagens; Mutation; Mycoses; Natural Immunity; Odds Ratio; Oncogenes; Open Reading Frames; Opportunistic Infections; Organ; Other Genetics; Outcome; Participant; Pathogenesis; Pathogenicity; Pathway interactions; Patients; Peer Review; Penetrance; Persons; Pharmacotherapy; Plasma; Population; Predisposition; Premature aging syndrome; Prevalence; Prevention; Primary carcinoma of the liver cells; Process; Prognostic Factor; Prognostic Marker; Prospective cohort; Proteins; Proteomics; Public Health; Publications; RNA; Research Design; Research Personnel; Retroelements; Retroviridae; Risk; Role; Sampling; Series; Severities; Sickle Cell Trait; Single-Stranded DNA; Somatic Mutation; South Africa; South African; Southern Africa; Sterol O-Acyltransferase; Subgroup; Susceptibility Gene; TP53 gene; Technology; Testing; The Cancer Genome Atlas; Time; Tissues; Tumor Suppressor Genes; Vaccines; Validation; Variant; Viral; Viral Load result; Virus Diseases; Virus Replication; Work; acquired immunity; antiretroviral therapy; carcinogenesis; cohort; differential expression; effective therapy; experience; follow-up; genetic variant; genome wide association study; global health; high risk; in vivo; infection rate; insight; lipid disorder; lipid metabolism; macrophage; malignant breast neoplasm; microRNA biomarkers; novel; outcome forecast; pandemic disease; prognostic signature; protective effect; protein expression; risk prediction model; risk variant; targeted treatment; tool; transcriptome sequencing; transcriptomics; transmission process; tumor

Our focus is on two major infectious diseases that impact 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 these infectious 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 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. 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) APOL1 variant alleles associate with reduced risk for opportunistic infections in HIV infection. Because APOL1 variants also dysregulate macrophage differentiation, we investigated the association of APOL1 with opportunistic infections in persons with HIV infection among 440 African Americans with HIV and performed a meta-analysis comprising 4 HIV/AIDS cohorts with 2066 participants. Carriage of two APOL1 variant alleles was associated with 71% reduction in odds of opportunistic infections. We validated this finding in the three HIV prospective cohorts in a meta-analysis. Carriage of two APOL1 variant alleles was associated with a 36% reduction in odds of opportunistic infections. Using a global test combining all four cohorts, carriage of two APOL1 variant alleles was associated with a 50% reduction in odds of opportunistic infections. Subgroup analysis of OI etiological categories revealed that OI protection is mainly attributable to specific protection from fungal infections. The study suggests a broader role of APOL1 variant alleles in innate immunity in vivo. Many patients with severe COVID-19 experience acute kidney injury requiring dialysis. We hypothesize that APOL1 renal high-risk genotypes and sickle cell trait, carried by 13% and 10% of African Americans, are associated with severity of AKI. Accomplishments in HBV-associated liver cancer: 1) We conducted the first study on the impact of the SOAT1 genetic variants and protein expression on HBV-related HCC. A recent proteomics study discovered a lipid metabolism enzyme Sterol O-acyltransferase (SOAT1) involvement in the progression of HCC. To assess the impact of SOAT1 gene variation on risk of HCC occurrence, we genotyped three protein-coding region SOAT1 variants, in 221 biopsy proven HCC patients and 229 healthy individuals. The V323V variant (OR) = 0.58, P = 0.04) and a haplotype TGA (OR = 0.40, P = 0.01) were associated with reduced HCC risk (42-60% lower risks) after adjusting for lipid levels. Using IHC, we found that the protein expression of SOAT1 was significantly increased in the tumor compared with adjacent tissue (P 0.001). This study revealed for the first time association of SOAT1 genetic variation with HBV-HCC susceptibility. This work is under peer-review for publication. 2) Our group also collaborated in a series of studies to identify prognostic biomarkers for HCC prognosis by providing assistance with study design and analysis. We helped identify competing endogenous RNA (ceRNA) network using dysregulated RNAs between tumor and adjacent liver tissues in 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). 3) There is a lack of validation 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 are valuable for development of targeted therapies and prevention once validated. 4) We are in the process identify microRNA markers for HCC diagnosis and prognosis. Detection of miRNA in serum/plasma can be a promising method for early HCC diagnosis enabling effective treatment. Collaborating with South African investigators, we are in the process using RNA-seq technology to systematically uncover the miRNA signatures in a cohort of HBV-associated HCC patients in South Africa. 5) Cytidine deaminases of the human APOBEC3 family (encoded by the APOBEC3 A-H genes) restrict retroviruses and mobile retroelements but also hypermutate host single strand (ss)DNA that may contribute to carcinogenesis. 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. A 29.5-kb DNA germline deletion that fuses the coding region of APOBEC3A with the 3'UTR of APOBCE3B. The APOBEC3B (A3B) deletion is common in Asian but rare in other populations, and is associated with elevated risk to breast cancer. We found this germline A3B deletion was associated with a 2-fold higher HCC risk and 3-5-fold higher risk for one or two-copy deletion compared with no deletion. This result indicates that the common A3B deletion is a major HCC susceptibility locus. We further found that A3B deletion carriers had 2-fold higher risk to have cirrhosis. As the effect of the A3B deletion is so strong and carriage rate is so high in Asian, where HCC prevalence is the highest in the world, an inclusion of the A3B in the polygenic HCC risk prediction model is warranted. We speculate that A3B may modify HCC risk through interacting with key cancer genes including tumor suppressor genes or oncogenes. We particularly explored the relationship between the A3B deletion and tumor suppressor gene TP53. We found a higher TP53 mutation rate among non-carriers of the A3B deletion compared with the two-copy A3B deletion carriers (24% vs. 9%, p=0.02), suggesting A3B presence may cause TP53 mutation, and that its absence reduces the chance of mutation, consistent with the A3B role as a hypermutator, a novel mechanism that links between A3B and HCC through TP53.

我们的重点是影响全球健康的两种主要传染病。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可以阻止HIV复制。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) APOL1变异等位基因与HIV感染中机会性感染风险降低相关。由于APOL1变异也会失调巨噬细胞分化，我们调查了440名非洲裔美国HIV感染者中APOL1与机会性感染的关系，并进行了一项包含4个HIV/AIDS队列的荟萃分析，其中包括2066名参与者。携带两个APOL1变异等位基因与机会性感染几率降低71%相关。在一项荟萃分析中，我们在三个HIV前瞻性队列中验证了这一发现。携带两个APOL1变异等位基因与机会性感染几率降低36%相关。通过结合所有四个队列的全球测试，携带两个APOL1变异等位基因与机会性感染几率降低50%相关。对成骨不全病因分类的亚组分析显示，成骨不全保护主要是由于对真菌感染的特异性保护。该研究提示APOL1变异等位基因在体内先天免疫中具有更广泛的作用。许多重症COVID-19患者会出现需要透析的急性肾损伤。我们假设13%和10%的非裔美国人携带APOL1肾高危基因型和镰状细胞性状与AKI的严重程度相关。1)首次开展了SOAT1基因变异及蛋白表达对hbv相关性肝癌的影响研究。最近的一项蛋白质组学研究发现脂质代谢酶甾醇o -酰基转移酶（SOAT1）参与HCC的进展。为了评估SOAT1基因变异对HCC发生风险的影响，我们在221例活检证实的HCC患者和229例健康个体中对三种蛋白质编码区SOAT1变异进行了基因分型。在调整脂质水平后，V323V变异(OR) = 0.58, P = 0.04)和单倍型TGA （OR = 0.40, P = 0.01）与HCC风险降低（42-60%风险降低）相关。通过免疫组化，我们发现SOAT1蛋白在肿瘤中的表达与邻近组织相比显著升高（P < 0.001）。本研究首次揭示了SOAT1基因变异与HBV-HCC易感性的相关性。这项工作正在接受同行评审，以便发表。2)我们小组还合作了一系列研究，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。我们利用TCGA中肿瘤和邻近肝组织之间的失调RNA，帮助鉴定竞争内源性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）。3)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。一旦被证实，已确定的途径和基因对靶向治疗和预防的发展有价值。4)我们正在寻找用于HCC诊断和预后的microRNA标志物。检测血清/血浆中的miRNA可能是早期HCC诊断和有效治疗的一种有前景的方法。与南非研究人员合作，我们正在使用RNA-seq技术系统地揭示南非hbv相关HCC患者队列中的miRNA特征。5)人类APOBEC3家族的胞苷脱胺酶（由APOBEC3 a - h基因编码）限制逆转录病毒和移动逆转录元件，但也可能导致宿主单链DNA的超突变，这可能有助于致癌。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。一个29.5 kb的DNA种系缺失，将APOBEC3A的编码区与APOBCE3B的3'UTR融合。APOBEC3B （A3B）缺失在亚洲人中很常见，但在其他人群中很少见，并且与乳腺癌风险升高有关。我们发现，与无缺失相比，这种种系A3B缺失与HCC风险高2倍相关，与单拷贝或双拷贝缺失的风险高3-5倍相关。这一结果表明常见的A3B缺失是HCC的主要易感位点。我们进一步发现A3B缺失携带者发生肝硬化的风险高出2倍。亚洲是世界上HCC患病率最高的地区，由于A3B缺失的影响如此之大，携带率如此之高，因此将A3B纳入多基因HCC风险预测模型是有必要的。我们推测A3B可能通过与肿瘤抑制基因或癌基因等关键癌症基因的相互作用来改变HCC的风险。我们特别探讨了A3B缺失与肿瘤抑制基因TP53之间的关系。我们发现，与A3B双拷贝缺失携带者相比，非A3B缺失携带者的TP53突变率更高（24% vs. 9%, p=0.02），提示A3B的存在可能导致TP53突变，而其缺失降低了突变的机会，这与A3B作为超突变者的作用一致，A3B是通过TP53将A3B与HCC联系起来的一种新机制。