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。 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肾风险变异与艾滋病毒强烈相互作用，导致艾滋病毒相关肾病，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）可阻碍 HIV 复制。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) 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 变异也会导致巨噬细胞分化失调，因此我们在 440 名 HIV 感染者中调查了 APOL1 与 HIV 感染者机会性感染的关系，并对 4 个 HIV/AIDS 队列的 2066 名参与者进行了荟萃分析。携带两个 APOL1 变异等位基因与机会性感染几率降低 71% 相关。我们通过荟萃分析在三个艾滋病毒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。对成骨不全病因类别的亚组分析表明，成骨不全的保护主要归因于对真菌感染的特异性保护。该研究表明 APOL1 变异等位基因在体内先天免疫中发挥更广泛的作用。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 肾脏高危基因型和镰状细胞性状，它们与 AKI 的严重程度相关。在HBV相关肝癌方面取得的成就：1）我们首次开展了SOAT1基因变异和蛋白表达对HBV相关HCC影响的研究。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) 参与了 HCC 的进展。为了评估 SOAT1 基因变异对 HCC 发生风险的影响，我们对 221 名活检证实的 HCC 患者和 229 名健康个体的三个蛋白质编码区 SOAT1 变异进行了基因分型。在调整血脂水平后，V323V 变体 (OR) = 0.58，P = 0.04）和单倍型 TGA（OR = 0.40，P = 0.01）与 HCC 风险降低（风险降低 42-60%）相关。使用IHC，我们发现肿瘤中SOAT1的蛋白表达与癌旁组织相比显着增加（P<0.001）。这项研究首次揭示了 SOAT1 基因变异与 HBV-HCC 易感性的关联。这项工作正在接受同行评审以供出版。 2) 我们小组还合作开展了一系列研究，通过提供研究设计和分析帮助来确定 HCC 预后的生物标志物。我们利用 TCGA 中肿瘤和邻近肝组织之间失调的 RNA 帮助识别竞争性内源性 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）。 3) 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。所确定的途径和基因一旦得到验证，对于开发靶向治疗和预防非常有价值。 4) 我们正在鉴定用于 HCC 诊断和预后的 microRNA 标记物。检测血清/血浆中的 miRNA 可能是早期 HCC 诊断的一种有前途的方法，从而实现有效的治疗。我们与南非研究人员合作，正在使用 RNA 测序技术系统地揭示南非一组 HBV 相关 HCC 患者的 miRNA 特征。 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，但也会使宿主单链 (ss)DNA 发生超突变，从而可能导致致癌。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中强内源性诱变剂。 29.5 kb 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相关。我们发现，与不删除相比，种系 A3B 删除与 HCC 风险高出 2 倍相关，而一或两个拷贝删除的风险则高出 3-5 倍。该结果表明常见的A3B缺失是HCC的主要易感位点。我们进一步发现A3B缺失携带者患肝硬化的风险高出2倍。由于 A3B 缺失的影响如此强烈，并且在亚洲（亚洲是世界上 HCC 患病率最高的地区）携带率如此之高，因此有必要将 A3B 纳入多基因 HCC 风险预测模型中。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相互作用来改变 HCC 风险。我们特别探讨了A3B缺失与抑癌基因TP53之间的关系。我们发现，与两拷贝 A3B 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），这表明 A3B 的存在可能导致 TP53 突变，而 A3B 的缺失则降低了突变的机会，这与 A3B 作为超突变子的作用一致，这是一种通过 TP53 连接 A3B 和 HCC 的新机制。