MALAT1 suppression is a hallmark of tissue and peripheral proliferative T cells in COVID-19

By Pooja Toshniwal PahariaJan 10 2023Reviewed by Aimee Molineux

In a recent study posted to the medRxiv* preprint server, researchers in the United Kingdom investigated lncRNA (long non-coding ribonucleic acids) expression in coronavirus disease 2019 (COVID-19) T lymphocyte transcriptomes.

Profiling lncRNA expression in immunological cells during the response to infection could provide insights into the main transcriptional and post-transcriptional pathways functional in health and illness. Transcriptomes of tissue and peripheral T lymphocytes during the response to infections, especially COVID-19, are well-characterized. However, data on the T lymphocyte lncRNA profiles are limited and require further investigation.

The authors of the present study previously showed that, among the cluster of differentiation 4+ (CD4+) T lymphocytes, MALAT1 (metastasis-associated lung adenocarcinoma transcript 1) gene suppression was characteristic of naïve CD4+ T lymphocyte (CD4_N) activation and that MALAT1-/- CD4+ T lymphocytes express the pro-inflammatory cytokine interleukin 10 (IL-10) in low amounts, in experimental malaria and leishmaniasis models.

Study: Down-regulation of MALAT1 is a hallmark of tissue and peripheral proliferative T cells in COVID-19. Image Credit: Chameleon Pictures / Shutterstock

This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources

About the study

The researchers extended their previous analysis by examining previously published single-cell RNA sequencing (scRNA seq) datasets from bronchoalveolar lavage (BAL), post-mortem pulmonary cells, and peripheral blood samples of individuals with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections.

T lymphocyte lncRNA profiles were explored from previously published scRNA-seq datasets (n=3) from SARS-CoV-2-positive individuals with lncRNAs detectable in pulmonary T lymphocytes during SARS-CoV-2 infection, emphasizing MALAT1. Gene signatures covarying with MALAT1 in T lymphocytes were identified based on gene set enrichment analysis. Post-mortem tissues of deceased COVID-19 patients from the UK-CIC (United Kingdom coronavirus immunology consortium, were subjected to RNAscope analysis, and UMAP (uniform manifold approximation and projection) analysis was performed.

Cell-type data were analyzed for fine-grained T lymphocyte phenotyping. To understand the effects of varying MALAT1 expression across fine-grained and coarse-grained T lymphocyte heterogeneity, the team assessed the correlation of MALAT1 expression with other genes for T lymphocyte subsets. Further, the team investigated whether the top 25 MALAT1-correlated genes and top 25 MALAT1-anti-correlated genes among CD4+ T lymphocytes and CD8+ T lymphocytes were expressed differentially in clusters previously identified or within imputed cellular subpopulations.

Results

The MALAT1 lncRNA showed the greatest transcription among T lymphocytes across all datasets, with type 1 T helper (Th1) lymphocytes showing the least and CD8+ resident memory lymphocytes the most significant MALAT1 expression, in CD4+ lymphocyte and CD8+ T lymphocyte populations, respectively. Significantly more transcripts showed a negative correlation with MALAT1 compared to those that showed positive correlations. MALAT1-anti-correlating genetic signatures showed enrichment of T lymphocyte activation, oxidative phosphorylation, cell division, and cytokine response genes.

The genetic signature anti-correlating with MALAT1, which was shared among CD4+ lymphocytes and CD8+ lymphocytes, marked replicating T lymphocytes in the blood and lung of SARS-CoV-2-positive individuals. MKI67 (the marker of proliferation Ki-67)-expressing CD8+ T lymphocytes had lower levels of MALAT1 mRNA in situ, indicating that lower MALAT1 expression was characteristic of MKI67+ replicating CD8-expressing T lymphocytes. MALAT1 correlated negatively with cell cycle progression and proliferation in CD4+ lymphocytes and CD8+ lymphocytes of patients with severe COVID-19.

Of interest, of the 10 lncRNAs with the greatest expression, only the MALAT1 lncRNA expression was reduced among individuals with severe COVID-19 relative to those with no or mild to moderate COVID-19. CD4+ Th1 lymphocytes showed lesser MALAT1 expression compared to naive CD4+ lymphocytes, whereas the regulatory CD4 lymphocytes and resident memory CD8+ lymphocytes subsets showed the greatest MALAT1 expression. Compared to effector memory CD8+ lymphocytes, exhausted CD8+ lymphocytes showed lower MALAT1 expression.

Eighty percent of genes, the expression of which significantly varied with MALAT1 expression, were the ones anti-correlating with MALAT1 expression in all T lymphocytes. The corresponding percentages were 88% and 65% for CD4+ lymphocytes and CD8+ lymphocytes in the case of correlation assessment for individual T lymphocyte populations. Of genes showing a positive correlation with MALAT1 expression for CD4+ lymphocytes and CD8+ lymphocytes, 79 genes were shared among CD4+ lymphocyte and CD8+ lymphocyte subtypes, and >4.0-fold higher distinct genes correlating with MALAT1 among CD8+ lymphocytes (n=210) over CD4+ ones (n=47) were detected.

Among CD4+ T lymphocytes, the expression of genes anti-correlating with MALAT1 expression was more significant in cluster 2, whereas a genetic signature with a strong positive correlation with MALAT1 was observed in cluster 0, cluster 1, and cluster 5. Cluster 2 cells mainly comprised CD4+ Th1 lymphocytes, whereas cells of cluster 0, cluster 1, and cluster 5 primarily comprised naive or effector memory CD4+ T lymphocytes. Similarly, among CD8+ T lymphocytes, cluster 2 mainly comprised MALAT1 anti-correlating genes. Exhausted CD8+ lymphocytes were enriched with MALAT1 anti-correlating genes, whereas MALAT1 correlated signature showed resident memory and effector memory CD8+ T lymphocyte CD8+ T lymphocyte enrichment.

Overall, the study findings showed that reduced MALAT1 expression was characteristic of proliferative T lymphocytes in COVID-19 patients.

This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources