Genome-wide characterization of alternative splicing in blood cells of COVID-19 and respiratory infections of relevance

Huang, Rui; Chen, Wenbo; Zhao, Xueya; Ma, Yuefei; Zhou, Qing; Chen, Junsen; Zhang, Muyi; Zhao, Dingran; Hou, Yu; He, Chunjiang; Wu, Ying

doi:10.1016/j.virs.2023.01.007

Cited by 4 publications

(6 citation statements)

References 25 publications

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“… 12 , 41 , 42 , 43 We also found that the variant- and vaccination-specific gene expression profiles of genes which are member of RNA splicing machinery, suggesting that global and variant specific regulation of AS is highly associated with transcriptional alterations of RNA binding proteins. 17 , 33 , 66 This further suggests that the observed splicing gene depression might underlie the abnormal AS seen in COVID-19 patients.…”

Section: Discussionmentioning

confidence: 86%

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Variant- and vaccination-specific alternative splicing profiles in SARS-CoV-2 infections

Lee,

Furth,

Hennighausen

et al. 2024

iScience

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Section: Discussionmentioning

confidence: 86%

“… 12 , 13 , 14 , 15 This is also true of SARS-CoV-2 infection. 11 , 15 , 16 , 17 , 18 Specific alternative spliced transcripts present with SARS-CoV-2 infection can lead to reduced antiviral immunity. Examples of previously identified alternatively spliced genes include CD74 and LRRFIP115, and OAS1.…”

Section: Introductionmentioning

confidence: 99%

Variant- and vaccination-specific alternative splicing profiles in SARS-CoV-2 infections

Lee,

Furth,

Hennighausen

et al. 2024

iScience

View full text Add to dashboard Cite

“…Secondly, the GO terms from the stage2 DD analysis are all pointing towards a immune response to a viral infection. The GO terms from the stage2 DE analysis are instead more generic terms, some of which have been reported previously to be enriched in COVID patients (e.g., peptide biosynthetic process (Huang et al, 2023), organonitrogen compound biosynthtic process (Jeyananthan, 2022), gene expression (Choudhary et al, 2021), cellular amide metabolic process (Huang et al, 2023), amide biosynthetic process (Li et al, 2021) and cellular macromolecule biosynthetic process (Huang et al, 2023)).…”

Section: Resultsmentioning

confidence: 99%

Differential detection workflows for multi-sample single-cell RNA-seq data

Gilis,

Perin,

Malfait

et al. 2023

Preprint

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In single-cell transcriptomics, differential gene expression (DE) analyses typically focus on testing differences in the average expression of genes between cell types or conditions of interest. Single-cell transcriptomics, however, also has the promise to prioritise genes for which the expression differ in other aspects of the distribution. Here we develop a workflow for assessing differential detection (DD), which tests for differences in the average fraction of samples or cells in which a gene is detected. After benchmarking eight different DD data analysis strategies, we provide a unified workflow for jointly assessing DE and DD. Using simulations and two case studies, we show that DE and DD analysis provide complementary information, both in terms of the individual genes they report and in the functional interpretation of those genes.

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“…It has been implicated in various diseases including viral infections, where it is poised to play a crucial role in modulating host immune responses and viral replication mechanisms [12][13][14][15] . This is also true of SARS-CoV-2 infection 11,[15][16][17][18] . Specific alternative spliced transcripts present with SARS-CoV-2 infection can lead to reduced antiviral immunity.…”

Section: Introductionmentioning

confidence: 87%

Variant- and Vaccination-Specific Alternative Splicing Profiles in SARS-CoV-2 Infections

Lee,

Furth,

Hennighausen

et al. 2023

Preprint

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SummaryThe COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, and its subsequent variants has underscored the importance of understanding the host-viral molecular interactions to devise effective therapeutic strategies. A significant aspect of these interactions is the role of alternative splicing in modulating host responses and viral replication mechanisms. Our study sought to delineate the patterns of alternative splicing of RNAs from immune cells across different SARS-CoV-2 variants and vaccination statuses, utilizing a robust dataset of 190 RNA-seq samples from our previous studies, encompassing an average of 212 million reads per sample. We identified a dynamic alteration in alternative splicing and genes related to RNA splicing were highly deactivated in COVID-19 patients and showed variant- and vaccination-specific expression profiles. Overall, Omicron-infected patients exhibited a gene expression profile akin to healthy controls, unlike the Alpha or Beta variants. However, significantly, we found identified a subset of infected individuals, most pronounced in vaccinated patients infected with Omicron variant, that exhibited a specific dynamic in their alternative splicing patterns that was not widely shared amongst the other groups. Our findings underscore the complex interplay between SARS-CoV-2 variants, vaccination-induced immune responses, and alternative splicing, emphasizing the necessity for further investigations into these molecular cross-talks to foster deeper understanding and guide strategic therapeutic development.

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Genome-wide characterization of alternative splicing in blood cells of COVID-19 and respiratory infections of relevance

Cited by 4 publications

References 25 publications

Variant- and vaccination-specific alternative splicing profiles in SARS-CoV-2 infections

Variant- and vaccination-specific alternative splicing profiles in SARS-CoV-2 infections

Differential detection workflows for multi-sample single-cell RNA-seq data

Variant- and Vaccination-Specific Alternative Splicing Profiles in SARS-CoV-2 Infections

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