MicroRNAs in long COVID: roles, diagnostic biomarker potential and detection

Abstract

Long COVID or Post-Acute Sequelae of SARS-CoV-2 Infection (PASC), marked by persistent symptoms lasting weeks to months after acute SARS-CoV-2 infection, affects multiple organ systems including the respiratory, cardiovascular, neurological, gastrointestinal, and renal systems. These prolonged effects stem from chronic inflammation, immune dysregulation, and direct viral injury. MicroRNAs (miRNAs)-small non-coding RNAs involved in gene regulation-play a pivotal role in this process by modulating immune responses, inflammation, and cellular stress. Altered miRNA expression patterns during and after infection contribute to the pathogenesis of Long COVID. While conventional miRNA detection techniques have been valuable, they face limitations in sensitivity, throughput, and detecting RNA modifications. This review highlights Oxford Nanopore Sequencing (ONS) as a promising alternative, offering real-time, long-read, amplification-free RNA sequencing that preserves native modifications. ONS enables direct sequencing of full-length miRNAs and their precursors, providing novel insights into miRNA processing and regulatory roles. Despite current challenges with short-read accuracy, ongoing technical advances are improving ONS performance. Its integration in miRNA profiling holds significant potential for uncovering novel regulatory interactions and advancing clinical biomarker discovery in Long COVID and other conditions.

Keywords: Biomarker discovery; Immune dysregulation; Inflammation; Nanopore sequencing; Noncoding RNA.

Fig. 1

Main signalling pathways in COVID-19 immunological response with participation of miRNAs after SARS-CoV-2’s binding by angiotensin-converting enzyme 2 (ACE2). TLR detect pathogen-associated molecular patterns and initiate inflammatory cytokines production via miRNAs; alternatively, TLR may directly bind SARS-CoV-2 spike protein. Abbreviations: ACE2, Angiotensin-converting enzyme 2; TLR, Toll like receptor; NF-kB, nuclear factor-kappa B; MAPK, mitogen-activated protein kinases; IFN γ, Interferon gamma; IL, interleukin; TNF-α, Tumor Necrosis Factor-alpha; IL-1β, Interleukin 1β, IL-6, Interleukin 6; BACH1, BTB and CNC homology 1; bZIP, basic leucine zipper transcription factor 1; SOCS1, suppressor of cytokine signalling 1; HIF-1α, hypoxia-inducible factor 1-alpha; ARG2, Arginase 2; ETS-1, Transformation-specific Sequence 1 factor; AGTR1, angiotensin II receptor type 1

Fig. 2

Specific miRNAs involvement in Long COVID occurrence and development in (i) the brain, where miR-124 promotes neuronal differentiation by repressing SCP1 and limits neuroinflammation via Signal Transducer and Activator of Transcription 3 (STAT3) and C/EBP-α; (ii) the lung, where miR-29 downregulates TGF-β1/Smad, PI3K/Akt/mTOR, and DNA methylation pathways, thus exerting anti-fibrotic and anti-inflammatory effects; miR-21 and miR-200 upregulate TGF-β1/Smad signaling, promoting pulmonary fibrosis and chronic inflammation; (iii) the heart, where upregulated miR-21 inhibits SPRY and PTEN and increased miR-29b-3p upregulates DNA Methyltransferase 3 Alpha (DNMT3A), collectively exacerbating myocarditis and heart failure; (iv) the kidney, where miR-192 and miR-200 upregulate TGF-β/Smad promoting renal fibrosis; and (v) the intestine, where miR-21 drives fibrotic extracellular-matrix production, miR-21-5p downregulate NF-κB/STAT3 to orchestrate immune responses. Abbreviations: TGF-β, Transforming Growth Factor Beta; Smad, Intracellular proteins mediating TGF-β signaling; PI3K, Phosphoinositide 3-Kinase; Akt, Protein Kinase B; mTOR, Mechanistic Target of Rapamycin; STAT3, Signal Transducer and Activator of Transcription 3; NF-κB, Nuclear Factor kappa-light-chain-enhancer of Activated B cells; CEBP-α, CCAAT/Enhancer-Binding Protein Alpha; SCP1, Small C-terminal domain Phosphatase 1; SPRY, Sprouty proteins (receptor tyrosine kinase signaling inhibitors); PTEN, Phosphatase and Tensin Homolog; DNMT3A, DNA Methyltransferase 3 Alpha

Fig. 3

Typical routes for miRNA detection using molecular analysis platforms (acronyms in the bottom row refer to online miRNA databases)