Functional Genomic Screening Identifies lncRNA CNPY2-AS1 as a Regulator of Redox Metabolism and Antiviral Immunity

Abstract

The human genome encodes thousands of long non-coding RNAs (lncRNAs) that regulate innate immunity and viral life cycles, yet their roles in viral entry remain understudied. Here, we conducted a genome-wide CRISPR interference screen to identify lncRNAs that regulate SARS-CoV-2 entry. We identified two lncRNAs that modulate angiotensin-converting enzyme 2 (ACE2) dependent viral entry through distinct mechanisms. Our findings suggest that the RP11-314A20.5 locus acts as a cis-regulatory element that modulates the expression of neighboring genes, including MED11 and CXCL16, linking this genomic region to host pathways associated with SARS-CoV-2 entry and COVID-19 severity. In contrast, CNPY2-AS1 functions in trans as a central regulator coupling cellular redox homeostasis to innate immune signaling. Mechanistically, CNPY2-AS1 associates with thioredoxin reductase 1 (TXNRD1), a key enzyme that limits reactive oxygen species. Loss of CNPY2-AS1 disrupts redox balance, triggering ligand-independent STAT1 activation and IRF7-mediated interferon and inflammatory responses. This dysregulated program has dual effects: induction of the interferon-stimulated gene PLSCR1 restricts viral entry by reducing cell-surface ACE2, while concurrent cytokine activation recapitulates features of pathological inflammation in severe COVID-19. Consistently, clinical datasets show reduced CNPY2-AS1 expression in patients with fatal disease. Together, these findings reveal distinct lncRNA-mediated mechanisms regulating SARS-CoV-2 entry and identify CNPY2-AS1 as a critical integrator of redox metabolism and innate antiviral immunity.