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Ring finger protein 39 genetic variants associate with HIV-1 plasma viral loads and its replication in cell culture.

ABSTRACT: BACKGROUND:The human immunodeficiency virus (HIV-1) exploits host proteins to complete its life cycle. Genome-wide siRNA approaches suggested that host proteins affect HIV-1 replication. However, the results barely overlapped. RING finger protein 39 (RNF39) has been identified from genome-wide association studies. However, its function during HIV-1 replication remains unclear. METHODS AND RESULTS:We investigated the relationship between common RNF39 genetic variants and HIV-1 viral loads. The effect of RNF39 protein knockdown or overexpression on HIV-1 replication was then investigated in different cell lines. Two genetic variants were associated with HIV-1 viral loads. Patients with the ht1-GG/GG haplotype presented lower RNF39 expression levels and lower HIV-1 viral load. RNF39 knockdown inhibited HIV-1 expression. CONCLUSIONS:RNF39 protein may be involved in HIV-1 replication as observed in genetic studies on patients with HIV-1 and in in vitro cell cultures.

SUBMITTER: Lin YJ

PROVIDER: S-EPMC4131809 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Ring finger protein 39 genetic variants associate with HIV-1 plasma viral loads and its replication in cell culture.

Lin Ying-Ju YJ Chen Chia-Yen CY Jeang Kuan-Teh KT Liu Xiang X Wang Jen-Hsien JH Hung Chien-Hui CH Tsang Hsinyi H Lin Ting-Hsu TH Liao Chiu-Chu CC Huang Shao-Mei SM Lin Cheng-Wen CW Ho Mao-Wang MW Chien Wen-Kuei WK Chen Jin-Hua JH Ho Tsung-Jung TJ Tsai Fuu-Jen FJ

Cell & bioscience 20140805

<h4>Background</h4>The human immunodeficiency virus (HIV-1) exploits host proteins to complete its life cycle. Genome-wide siRNA approaches suggested that host proteins affect HIV-1 replication. However, the results barely overlapped. RING finger protein 39 (RNF39) has been identified from genome-wide association studies. However, its function during HIV-1 replication remains unclear.<h4>Methods and results</h4>We investigated the relationship between common RNF39 genetic variants and HIV-1 vira ...[more]

PMID: 25126410

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Project description:Quantification of HIV RNA in plasma is critical for identifying the disease progression and monitoring the effectiveness of antiretroviral therapy. While RT-qPCR has been the gold standard for HIV viral load quantification, digital assays could provide an alternative calibration-free absolute quantification method. Here, we reported a Self-digitization Through Automated Membrane-based Partitioning (STAMP) method to digitalize the CRISPR-Cas13 assay (dCRISPR) for amplification-free and absolute quantification of HIV-1 viral RNAs. The HIV-1 Cas13 assay was designed, validated, and optimized. We evaluated the analytical performances with synthetic RNAs. With a membrane that partitions ∼100 nL of reaction mixture (effectively containing 10 nL of input RNA sample), we showed that RNA samples spanning 4 orders of dynamic range between 1 fM (∼6 RNAs) to 10 pM (∼60k RNAs) could be quantified as fast as 30 min. We also examined the end-to-end performance from RNA extraction to STAMP-dCRISPR quantification using 140 μL of both spiked and clinical plasma samples. We demonstrated that the device has a detection limit of approximately 2000 copies/mL and can resolve a viral load change of 3571 copies/mL (equivalent to 3 RNAs in a single membrane) with 90% confidence. Finally, we evaluated the device using 140 μL of 20 patient plasma samples (10 positives and 10 negatives) and benchmarked the performance with RT-PCR. The STAMP-dCRISPR results agree very well with RT-PCR for all negative and high positive samples with Ct < 32. However, the STAMP-dCRISPR is limited in detecting low positive samples with Ct > 32 due to the subsampling errors. Our results demonstrated a digital Cas13 platform that could offer an accessible amplification-free quantification of viral RNAs. By further addressing the subsampling issue with approaches such as preconcentration, this platform could be further exploited for quantitatively determining viral load for an array of infectious diseases.

Dataset Information

Ring finger protein 39 genetic variants associate with HIV-1 plasma viral loads and its replication in cell culture.

Publications

Ring finger protein 39 genetic variants associate with HIV-1 plasma viral loads and its replication in cell culture.

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