Cellular Proteo-Transcriptomic Changes in the Immediate Early-Phase of Lentiviral Transduction

Abstract

Lentivirus-based vectors derived from human immunodeficiency viruses type 1 and 2 (HIV-1 and 2) are widely used tools in research and may also be utilized in clinical settings. Like their parental virions, they are known to depend on the cellular machinery for successful gene delivery and integration. While most of the studies on cellular proteomic and transcriptomic changes have focused on the late phase of the transduction, studies of those changes in early time-points, especially in the case of HIV-2 based vectors, are widely lacking. Using second generation HIV-1 and 2 vesicular stomatitis virus G protein (VSV-G) pseudotyped lentiviral vectors, we transduced HEK-293T human embryonic kidney cells and carried out transcriptomic profiling at 0 and 2 h time points, with accompanying proteomic analysis at 2 h following transduction. Significant variations were observed in gene expression profile between HIV-1 and HIV-2 transduced samples. Thrombospondin 1 (THBS1), collagens (COL1A2, COL3A1), and eukaryotic translation factors (EIF3CL) in addition to various genes coding for long non-coding RNA (lncRNA) were significantly upregulated 2 h after HIV-2 transduction compared to HIV-1. Label-free quantification mass spectrometry (MS) indicated that seven proteins involved in RNA binding, mRNA transport, and chaperoning were significantly downregulated. The identification of cellular protein targets of lentiviral vectors and their effect on the cellular transcriptome will undoubtedly shed more light on their complex life cycle and may be utilized against infection by their parental lentiviruses. Furthermore, characterizing the early phase of HIV-2 infection may aid in the understanding of its pathomechanism and long incubation period.

Transcriptome‐wide profile of 1α,25 dihydroxyvitamin D3 in HTR‐8/SVneo cells

“…Chen et al 39 found that silencing EIF3CL downregulated phosphorylation of adenosine 5′‐monophosphate‐activated protein kinase α and nuclear factor kappa‐B p65, inhibited diffuse intrinsic pontine glioma cell proliferation and anchorage‐independent growth, and induced tumor cell apoptosis. Transcriptome analysis of human embryonic kidney cells transduced with human immunodeficiency viruses type 1 (HIV‐1) and 2 vesicular stomatitis virus G protein pseudotyped lentiviral vectors for 2 h found that EIF3CL was significantly upregulated after HIV‐2 transduction compared with HIV‐1 40 . At present, the research on EIF3CL and 1,25(OH) 2 D 3 needs to be further developed.…”

“…Transcriptome analysis of human embryonic kidney cells transduced with human immunodeficiency viruses type 1 (HIV-1) and 2 vesicular stomatitis virus G protein pseudotyped lentiviral vectors for 2 h found that EIF3CL was significantly upregulated after HIV-2 transduction compared with HIV-1. 40 At present, the research on EIF3CL and 1,25(OH) 2 D 3 needs to be further developed. ABCD2 is involved in the transport of long-chain and very longchain fatty acids (VLCFA) or their coenzyme A derivatives into peroxisomes with different substrate specificity.…”

Comparative Analysis of Differential Cellular Transcriptome and Proteome Regulation by HIV-1 and HIV-2 Pseudovirions in the Early Phase of Infection

“…In our previous publication, we described that changes generated by transduction with HIV-2 pseudovirions were significantly different from those generated by HIV-1 [ 43 ]. Indeed, this pattern was also noticed in later time-points as well.…”

ASCL1 Is Involved in the Pathogenesis of Schizophrenia by Regulation of Genes Related to Cell Proliferation, Neuronal Signature Formation, and Neuroplasticity

“…We expected the mutant gene to be transcribed into truncated transcripts that would not be translated, resulting in a functional knockout of ASCL1. To account for possible changes in the cell transcriptome caused by the transduction of lentiviral vectors [21], we also obtained a control cell line stably expressing sgRNA not directed against any of the targets in the human genome (non-target control, NTC). Given the role of ASCL1 in early neurodevelopment, these data suggest that ASCL1 is a promising candidate gene whose dysfunction leads to early events predisposing to SZ or other neuropsychiatric disorders.…”

“…We expected the mutant gene to be transcribed into truncated transcripts that would not be translated, resulting in a functional knockout of ASCL1. To account for possible changes in the cell transcriptome caused by the transduction of lentiviral vectors [21], we also obtained a control cell line stably expressing sgRNA not directed against any of the targets in the human genome (non-target control, NTC).…”