Limited TCR repertoire and ENTPD1 dysregulation mark late-stage COVID-19

Abstract

T-cell exhaustion and dysfunction are hallmarks of severe COVID-19. To gain insights into the pathways underlying these alterations, we performed a comprehensive transcriptome analysis of peripheral-blood-mononuclear-cells (PBMCs), spleen, lung, kidney, liver and heart obtained at autopsy from COVID-19 patients and matched controls, using the nCounter-CAR-T-Characterization panel. We found substantial gene alterations in COVID-19-impacted organs, especially the lung where altered TCR repertoires are noted. Reduced TCR repertoires are also observed in PBMCs of severe COVID-19 patients. ENTPD1/CD39 , an ectoenzyme defining exhausted T-cells, is upregulated in the lung, liver, spleen and PBMCs of severe COVID-19 patients where expression positively correlates with markers of vasculopathy. Heightened ENTPD1/CD39 is paralleled by elevations in STAT-3 and HIF-1α transcription factors; and by markedly reduced CD39 -antisense-RNA, a long-noncoding-RNA negatively regulating ENTPD1/CD39 at the post-transcriptional level. Limited TCR repertoire and aberrant regulation of ENTPD1/CD39 could have permissive roles in COVID-19 progression and indicate potential therapeutic targets to reverse disease.

Alterations in CD39/CD73 axis of T cells associated with COVID‐19 severity

“…These data indicate a failure in the immunosuppressive axis of adenosine generation by Treg cells during SARS‐CoV‐2 infection. Contrary to us, an upregulation in ENTPD1 (CD39) gene expression within the Treg pathway in peripheral tissues of severe COVID‐19 patients was previously reported, suggesting higher Treg suppression mediated by the CD39 axis may occur in the infected tissues during acute SARS‐CoV‐2 infection that may contribute to secondary infections by others pathogens (Wang, Veurich, Kalbasi, Shaefi, et al, 2021 ). On the other hand, Meckiff et al ( 2020 ) described an imbalance of Tregs cells and cytotoxic reactive CD4 + T cells in severe COVID‐19.…”

“…In COVID‐19 patients, higher CD39 + T‐cell frequency was previously associated with the expression of PD‐1, confirming the hypotheses that SARS‐CoV‐2 infection induces a hyperactivated exhausted lymphocyte profile (Mathew, Giles, Baxter, Greenplate, et al, 2020 ), contributing to the T‐cell dysfunction in COVID‐19. Interestingly, Wang, Veurich, Kalbasi, Graham, et al ( 2021 ) identified increased CD39 expression in the lung, liver, spleen, and PBMCs from severe COVID‐19 patients, which correlated with days in the hospital, days in intensive care unit (ICU), and markers of coagulation, indicating associations between ectonucleotidases and disease progression. Similarly, CD39 messenger RNA (mRNA) as upregulated in peripheral blood leukocytes in association with higher soluble CD39 levels in severe COVID‐19 patients, which were related to the length of hospital day and ICU admission (Díaz‐García et al, 2022 ).…”

“…Similarly, CD39 messenger RNA (mRNA) as upregulated in peripheral blood leukocytes in association with higher soluble CD39 levels in severe COVID‐19 patients, which were related to the length of hospital day and ICU admission (Díaz‐García et al, 2022 ). Furthermore, upregulation in CD39 expression in late‐stage COVID‐19 was associated with heightened levels of STAT‐3 and HIF‐1α, but decreased levels of CD39‐antisense RNA, possibly a purinergic imbalance that contributes to metabolic changes and T‐cell dysfunction (Wang, Veurich, Kalbasi, Shaefi, et al, 2021 ). CD4 + CD39 + T cells identify an effector lymphocyte that is prone to apoptosis in older adults (Fang et al, 2016 ), corroborating with our data regarding higher apoptosis rate in the CD4 + T cells of COVID‐19 patients.…”

High Frequencies of PD-1+TIM3+TIGIT+CTLA4+ Functionally Exhausted SARS-CoV-2-Specific CD4+ and CD8+ T Cells Associated with Severe Disease in Critically ill COVID-19 Patients

“…In fact, those two epitopes have their slopes S the closest to 0 among all epitopes (Supplemental (ii) a general lymphopenia (11)(12)(13)(14)(15)(16); and (iii) a broad (not SARS-CoV-2-specific T cell exhaustion and/or impaired function (15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32). This was reported for immune cells both in the peripheral compartment (PBMCs) and in the lung and brain of symptomatic patients (13,69). The association of T cell exhaustion with COVID-19 severity is under debate with one study reporting no clear significant correlation with disease severity (70) (using a small number of patients) while two other reports, also using a small cohort of patients, discounted the link between higher expression exhaustion markers and impaired function of SARS-CoV-2specific CD4 + and CD8 + T cells in convalescent patients (71,72).…”

Parallel Dysregulated Immune Response in Severe Forms of COVID-19 and Bacterial Sepsis via Single-Cell Transcriptome Sequencing

“…Therefore, single-cell data analyses that are performed differently at the single-cell level compared with the cell population level can provide a clinical added value. This method can effectively identify transcriptomic differences that reflect immunosuppression and low-grade inflammation trajectories between patients with bacterial versus viral sepsis [ 32 , 33 , 34 ], with specific consideration given to the level of expression of cytotoxic genes in those critically ill, severe manifestations and the overexpression of genes [ 35 ] involved during sepsis that cause the efficient clearance of invading pathogens. These patient cohort differences at the single-cell level can guide the use of immunomodulatory therapy [ 36 ], addressing both the scale of severity and the progression of disease by displaying specific functional diversity and the downregulation of effector functions [ 37 , 38 ].…”