Interplay between SARS‐CoV‐2 and human long non‐coding RNAs

Abstract

The long non‐coding RNAs (lncRNAs) play a critical regulatory role in the host response to the viral infection. However, little is understood about the transcriptome architecture, especially lncRNAs pattern during the SARS‐CoV‐2 infection. In the present study, using publicly available RNA sequencing data of bronchoalveolar lavage fluid (BALF) and peripheral blood mononuclear cells (PBMC) samples from COVID‐19 patients and healthy individuals, three interesting findings highlighted: (a) More than half of the interactions between lncRNAs‐PCGs of BALF samples established by three trans‐acting lncRNAs (HOTAIRM1, PVT1 and AL392172.1), which also exhibited the high affinity for binding to the SARS‐CoV‐2 genome, suggesting the major regulatory role of these lncRNAs during the SARS‐CoV‐2 infection. (b) lncRNAs of MALAT1 and NEAT1 are possibly contributed to the inflammation development in the SARS‐CoV‐2 infected cells. (c) In contrast to the 3′ part of the SARS‐CoV‐2 genome, the 5′ part can interact with many human lncRNAs. Therefore, the mRNA‐based vaccines will not show any side effects because of the off‐label interactions with the human lncRNAs. Overall, the putative functionalities of lncRNAs can be promising to design the non‐coding RNA‐based drugs and to inspect the efficiency of vaccines to overcome the current pandemic.

Long Noncoding RNAs as Emerging Regulators of COVID-19

“…Due to the apparent similarity between SARS-CoV-2 and SARS-CoV, it can be speculated that lncRNAs have differential transcription in response to SARS-CoV-2 infection. Meanwhile, a large number of abnormal expressions of lncRNAs were found in bronchoalveolar lavage fluid (BALF) and peripheral blood mononuclear cells (PBMC) from COVID-19 patients in recent studies, which further verified this idea (8).…”

“…In addition, the differential expression of lncRNA may reflect the physiological and pathological changes of human body. For instance, lncRNAs NEAT1 and MALAT1, were significantly upregulated in BALF samples from patients compared to healthy samples, which have been shown to be potential biomarkers for HIV infection (8,105). The further investigation revealed that both lncRNAs were negatively correlated with CAPN1, a cysteine protease involved in the influenza virus infection.…”

“…The lncRNA NORAD can target five of the ten cytokines involved in cytokine storms and is thus involved in cytokine storms (44). In addition, the lncRNA MALAT1 is highly likely to regulate lung inflammatory injury caused by cytokines through the NF-kB, and can also target and down-regulate CAPN1, participating in viral infection (8,(93)(94)(95). Moreover, some viruses can spread from the lungs to the central nervous system via a blood-borne route.…”

“…In patients with SARS-CoV-2, several lncRNAs play major regulatory roles in the process of virus infection. For example, lncRNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and nuclear paraspeckle assembly transcript 1 (NEAT1) have been shown to be highly associated with the immune responses and that possibly involved in the inflammatory progression of SARS-CoV-2 infected cells (8,9). Furthermore, MALAT1 alleviated deep vein thrombosis (DVT) by inhibiting the proliferation and migration of endothelial progenitor cells (EPCs) and involved in thrombosis dissolution via regulating the Wnt/b-catenin signaling pathway (10).…”

Genome interaction of the virus and the host genes and non-coding RNAs in SARS-CoV-2 infection

“… Alam and Lipovich, 2021 , Arora et al, 2020 , Calcagnile et al, 2021 , Chow and Salmena, 2020 , Cipolla et al, 2018 , COVID-19 Host Genetics Initiative, 2020 , Hardenberg and Luft, 2020 , Hoffmann et al, 2020 , Hosseini Rad Sm and McLellan, 2020 , Hubacek et al, 2021 , Laha et al, 2021 , Li et al, 2020a , Li et al, 2021 , Li et al, 2020b , Liu et al, 2020a , Liu et al, 2020b , Lorente et al, 2021 , Ma et al, 2015 , Matyášek and Kovařík, 2020 , Menon and Hua, 2020 , Moazzam‐Jazi et al, 2021 , Paniri et al, 2021 , Paniri and Akhavan-Niaki, 2020 , Saçar Demirci and Adan, 2020 , Torre‐Fuentes et al, 2021 , Volz et al, 2021 , Walensky et al, 2021 , Xue et al, 2019 , Zeberg and Pääbo, 2020 .…”