Mucosal antigen-specific T cells are pivotal for pathogen clearance and immune modulation in respiratory infections. Dysregulated T cell responses exacerbate coronavirus disease 2019 severity, marked by cytokine storms and respiratory failure. Despite extensive description in peripheral blood, the characteristics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific T cells in the lungs remain elusive. Here we conducted integrated single-cell profiling of SARS-CoV-2-specific T cells in 122 bronchoalveolar lavage fluid (BALF) and 280 blood samples from 159 patients, including 27 paired BALF and blood samples from 24 patients. SARS-CoV-2-specific T cells were robustly elicited in BALF irrespective of prior vaccination, correlating with diminished viral loads, lessened systemic inflammation and improved respiratory function. SARS-CoV-2-specific T cells in BALF exhibited profound activation, along with proliferative and multi-cytokine-producing capabilities and a glycolysis-driven metabolic signature, which were distinct from those observed in peripheral blood mononuclear cells. After viral clearance, these specific T cells maintained a polyfunctional tissue-resident memory phenotype, highlighting their critical roles in infection control and long-term protection.

BACKGROUND

Urinary tract infections (UTIs) rank among the most prevalent bacterial infections globally. Traditional urine culture methods have significant limitations in detection time and sensitivity, prompting the need to evaluate targeted next-generation sequencing (tNGS) as a potential diagnostic tool.

METHODS

The study included a discovery cohort of 400 suspected UTI patients (202 analyzed) and a validation cohort of 200 patients (110 analyzed). The study assessed detection time, concordance rates, ability to identify polymicrobial infections, and antibiotic resistance genes (ARGs). Both clear and turbid urine samples were evaluated across different clinical settings.

RESULTS

In the discovery cohort, tNGS demonstrated 96.5% concordance with culture-positive samples, while showing superior specificity in culture-negative specimens (53.1% vs 28.1% for mNGS). Detection time for tNGS (12.89h) was notably shorter than mNGS (17.38h) and traditional culture (61.48h). tNGS exhibited remarkable capability in identifying polymicrobial infections (55.4% of samples), significantly outperforming both mNGS (27.7%) and traditional culture methods, which failed to detect any co-infections. The method showed particular strength in detecting fastidious organisms like Ureaplasma parvum and fungal species such as Candida tropicalis. For antibiotic resistance prediction, tNGS detected more ARGs (52.67% vs 41.22% for mNGS) and achieved 100% sensitivity for vancomycin and methicillin resistance in Gram-positive pathogens. The validation cohort confirmed tNGS's robust performance, maintaining high concordance rates for both culture-positive (90.00%) and culture-negative samples (55.00%), demonstrating consistent reliability across different clinical settings

CONCLUSIONS

tNGS demonstrates advantages in rapid and accurate UTI diagnosis, particularly in detecting polymicrobial infections and analyzing antibiotic resistance genes. It shows promise as an effective complementary tool for UTI diagnostics.

The precise regulation of the RIG-I-like receptors (RLRs)-mediated type I interferon (IFN-I) activation is crucial in antiviral immunity and maintaining host immune homeostasis in the meantime. Here, the authors identify an E3 ubiquitin ligase, namely RNF167, as a negative regulator of RLR-triggered IFN signaling. Mechanistically, RNF167 facilitates both atypical K6- and K11-linked polyubiquitination of RIG-I/MDA5 within CARD and CTD domains, respectively, which leads to degradation of the viral RNA sensors through dual proteolytic pathways. RIG-I/MDA5 conjugated with K6-linked ubiquitin chains in CARD domains is recognized by the autophagy cargo adaptor p62, that delivers the substrates to autolysosomes for selective autophagic degradation. In contrast, K11-linked polyubiquitination in CTD domains leads to proteasome-dependent degradation of RLRs. 

Thus, this study clarifies a function of atypical K6- and K11-linked polyubiquitination in the regulation of RLR signaling. The authors also unveil an elaborate synergistic effect of dual proteolysis systems to control amplitude and duration of IFN-I activation, hereby providing insights into physiological roles of the cross-talk between these two protein quality control pathways.

Chemo-immunotherapy is the current first-line treatment for patients with extensive-stage small cell lung cancer (ES-SCLC), but survival benefits are modest. The authors aimed to evaluate the safety, antitumor activity and biomarkers of first-line camrelizumab and apatinib plus chemotherapy in untreated ES-SCLC patients. In this single-arm trial (ClinicalTrials.gov NCT05001412), eligible patients received 2 cycles of etoposide and carboplatin (EC) as induction treatment followed by 2–4 cycles of camrelizumab, apatinib plus EC, then maintenance camrelizumab plus apatinib. Primary endpoint was safety. Secondary endpoints included objective response rate (ORR), duration of response, progression-free survival (PFS), and overall survival (OS). Targeted sequencing and whole transcriptome sequencing were performed to explore biomarkers. All enrolled 40 patients were treated and analyzed for safety. During the entire treatment, treatment-emergent adverse events (TEAEs) occurred in 40 patients (100%), and 30 (75.0%) were grade ≥3. The most common grade ≥3 TEAEs were neutropenia (35.0%), anemia (15.0%) and increased alanine aminotransferase (15.0%). No treatment-related deaths occurred. Among 36 evaluable patients, ORR was 88.9% (95% CI: 73.9%–96.9%), median PFS was 7.3 months (95% CI: 6.6–9.2) and median OS was 17.3 months (11.8-not reached). Mutations in RB1, high levels of tumor mutation burden, natural killer cells, and interferons, and low levels of cancer-associated fibroblasts, correlated with prolonged PFS. Induction chemotherapy followed by camrelizumab, apatinib plus EC demonstrated acceptable safety and promising antitumor activity in untreated ES-SCLC patients. The identified biomarkers need further validation.