EBioMedicine

It is estimated that approximately one-fourth of the world's population is infected with strains of the Mycobacterium tuberculosis complex (MTBC), the causative agents of tuberculosis (TB). In this study, we present rationally developed molecular markers for bacterial burden, which are derived from mycobacterial phospholipids. Using lipidomic approaches, we show that tuberculostearic acid (TSA)-containing phosphatidylinositols (PI) are present in all clinically relevant MTBC lineages investigated. For the major abundant lipid PI 16:0_19:0 (TSA), a detection limit equivalent to 102 colony forming units (CFU) was determined for bacterial cultures and approximately 103 for cell culture systems. We further developed a mass spectrometry based targeted lipid assay, which - in contrast to bacterial quantification on solid medium - can be performed within several hours including sample preparation. Translation of this indirect and culture-free detection approach allowed the determination of pathogen loads in infected murine macrophages, human neutrophils and murine lung tissue. We show that marker lipids inferred from the mycobacterial PIs are increased in peripheral blood mononuclear cells (PBMCs) of TB patients beyond the lipid metabolic background in comparison to healthy controls. In a small cohort of drug-susceptible TB patients elevated levels of these marker molecules were detected at therapy start and declined following successful anti-tuberculosis treatment. The concentration of TSA-containing PIs can be used as correlate for reliable and rapid quantification of Mycobacterium tuberculosis (Mtb) burden in experimental in vitro model systems and may also provide a clinically relevant tool for monitoring TB therapy. One Sentence SummaryTuberculostearic acid containing phosphatidylinositols represent a novel, fast to measure, reliable correlate of Mycobacterium tuberculosis bacterial burden in experimental model systems, which makes a future clinical application conceivable.

The tumor microenvironment (TME) of lung adenocarcinoma (LUAD) precursor lesions has not been described. We interrogated by multiplex immunofluorescence the TME of preinvasive and invasive Stage 1A LUADs selected by computer tomography (CT) scan-density. Pure non-solid (p-NS) CT density nodules are preinvasive/minimally invasive, whereas solid CT density nodules are frankly invasive cancers. Our data reveal an intensely immune-suppressive immune TME in p-NS tumors characterized by an increase in Treg cells and a decrease in cytotoxic T cells relative to normal lung. The TME of the solid tumor group, more advanced lesions than the p-NS yet still early in disease development, were increasingly more immune-suppressive. Provocatively, there was a further increase in both Treg cells and cytotoxic T cells, establishing a nascent albeit ineffective anti-tumor immune response in transition from preinvasive p-NS to invasive solid tumors. Regulatory T cells play a dominant role throughout progression, while additional immune evasive mechanisms are employed at different stages of disease progression, including T cell exclusion from cancer cell nests early and activation of immune checkpoints later. Our study establishes that different immune-targeted strategies are required to intercept disease progression at these two distinct early points of lung cancer development. Statement of SignificanceUsing multiplexed IF, we compared the cellular composition and activation state of the tumor immune microenvironment between pre/minimally invasive and frankly invasive adenocarcinoma. We found a progressive increase in immunosuppressive mechanisms in association with disease progression suggesting that Interception strategies should be specifically tailored based on underlying immune escape mechanisms

Rationale and ObjectivesThe extent and commonality of peripheral blood immune aberrations in fibrotic interstitial lung diseases are not well characterized. In this study, we aimed to identify common and distinct immune aberrations in patients with idiopathic pulmonary fibrosis (IPF) and fibrotic hypersensitivity pneumonitis (FHP) using cutting-edge single-cell profiling technologies. MethodsSingle-cell RNA sequencing was performed on patients and healthy controls peripheral blood and bronchoalveolar lavage samples using 10X Genomics 5 gene expression and V(D)J profiling. Cell type composition, transcriptional profiles, cellular trajectories and signaling, and T and B cell receptor repertoires were studied. The standard Seurat R pipeline was followed for cell type composition and differential gene expression analyses. Transcription factor activity was imputed using the DoRothEA-VIPER algorithm. Pseudotime analyses were conducted using Monocle3, while RNA velocity analyses were performed with Velocyto, scVelo, and CellRank. Cell-cell connectomics were assessed using the Connectome R package. V(D)J analyses were conducted using CellRanger and Immcantation frameworks. Across all analyses, disease group differences were assessed using the Wilcoxon rank-sum test. Measurements and Main Results327,990 cells from 83 samples were profiled. Overall, changes in monocytes were common to IPF and FHP, whereas lymphocytes exhibited disease-specific aberrations. Both diseases displayed enrichment of CCL3hi/CCL4hi CD14+ monocytes (p<2.2e-16) and S100Ahi CD14+ monocytes (p<2.2e-16) versus controls. Trajectory and RNA velocity analysis suggested that pro-fibrotic macrophages observed in BAL originated from peripheral blood monocytes. Lymphocytes exhibited disease-specific aberrations, with CD8+ GZMKhi T cells and activated B cells primarily enriched in FHP patients. V(D)J analyses revealed unique T and B cell receptor complementarity-determining region 3 (CDR3) amino acid compositions (p<0.05) in FHP and significant IgA enrichment in IPF (p<5.2e-7). ConclusionsWe identified common and disease-specific immune mechanisms in IPF and FHP; S100Ahi monocytes and SPP1hi macrophages are common to IPF and FHP, whereas GMZKhi T lymphocytes and T and B cell receptor repertoires were unique in FHP. Our findings open novel strategies for the diagnosis and treatment of IPF and FHP.

BackgroundMethylthioadenosine phosphorylase (MTAP) loss co-occurs with actionable genomic alterations in non-small cell lung cancer (NSCLC) and creates vulnerability to protein arginine methyltransferase 5 (PRMT5) inhibition. Estimates of prevalence of MTAP loss rely on next-generation sequencing which can underestimate copy losses. Moreover, the activity of PRMT5 inhibitors in oncogene-driven NSCLC is not well established. MethodsWe assessed MTAP expression by immunohistochemistry (IHC) in 243 NSCLCs (n=132 early stage, n=111 metastatic), including 33 specimens with paired lymph nodes. Antiproliferative activity of PRMT5 inhibitor monotherapy and in combination with tyrosine kinase inhibitors (TKIs) was evaluated in MTAP-deleted NSCLC cell lines harboring EGFR or KRAS mutations or ALK rearrangements. ResultsAmong 243 NSCLC specimens from 240 patients (72% with driver alterations, 90% adenocarcinoma), MTAP loss was identified in 43 (18%) specimens from 40 (17%) patients, including 18 (14%) early-stage and 22 (20%) metastatic tumors. MTAP loss occurred in 24% of stage 4 driver-positive NSCLCs versus 14% of driver-negative tumors (p=0.314). Twenty (61%) lung-nodal pairs demonstrated concordance; eight cases only exhibited decreased MTAP expression in nodes. Variable sensitivity to PRMT5 inhibitors was observed in 22 MTAP-deleted NSCLC cell lines (9 EGFR-mutant, 7 KRAS-mutant, 6 ALK-rearranged), with responses seen in TKI-sensitive and TKI-resistant lines. SDMA (symmetric dimethylarginine) expression did not predict PRMT5 inhibitor sensitivity. TKI + PRMT5 inhibitor combos had greater activity than monotherapy. ConclusionsMTAP loss occurs in 1-in-5 oncogene-driven metastatic NSCLCs. PRMT5 inhibitor activity is independent of TKI exposure, driver alteration, and SDMA expression and enhanced by addition of TKI. These findings support clinical evaluation of PRMT5 inhibitor + TKI combinations for advanced NSCLC.

Assessing autophagy promises to provide valuable information regarding the pathogenesis of chronic obstructive pulmonary disease (COPD). However, measuring the dynamic aspect of autophagy is challenging, and sample manipulation can cause signal fluctuations that deviate from the situation in vivo. Our aim was to assess an organotypic method to quantify autophagy in the context of COPD, where autophagy has demonstrated disease-related modulation. Blood from control and COPD participants was treated with/out chloroquine. Protein from peripheral blood mononuclear cells (PBMC) was then isolated and compared for LC3B-II abundance. Our observations show that while basal level LC3B-II abundance was similar between each group (P = 0.60), autophagic flux was significantly lower in the COPD cohort, suggesting disruption in autophagy (P = 0.004). We aim to extend this inquiry and compare pulmonary vs blood samples, to identify the utility of measuring autophagy in blood as a diagnostic outcome predictive of early COPD.

The novel coronavirus SARS-CoV-2 was identified as the causative agent of the ongoing pandemic COVID 19. COVID-19-associated deaths are mainly attributed to severe pneumonia and respiratory failure. Recent work demonstrated that SARS-CoV-2 binds to angiotensin converting enzyme 2 (ACE2) in the lung. To better understand ACE2 abundance and expression patterns in the lung we interrogated our in-house single-cell RNA-sequencing dataset containing 70,085 EPCAM+ lung epithelial cells from paired normal and lung adenocarcinoma tissues. Transcriptomic analysis revealed a diverse repertoire of airway lineages that included alveolar type I and II, bronchioalveolar, club/secretory, quiescent and proliferating basal, ciliated and malignant cells as well as rare populations such as ionocytes. While the fraction of lung epithelial cells expressing ACE2 was low (1.7% overall), alveolar type II (AT2, 2.2% ACE2+) cells exhibited highest levels of ACE2 expression among all cell subsets. Further analysis of the AT2 compartment (n = 27,235 cells) revealed a number of genes co-expressed with ACE2 that are important for lung pathobiology including those associated with chronic obstructive pulmonary disease (COPD; HHIP), pneumonia and infection (FGG and C4BPA) as well as malarial/bacterial (CD36) and viral (DMBT1) scavenging which, for the most part, were increased in smoker versus light or non-smoker cells. Notably, DMBT1 was highly expressed in AT2 cells relative to other lung epithelial subsets and its expression positively correlated with ACE2. We describe a population of ACE2-positive AT2 cells that co-express pathogen (including viral) receptors (e.g. DMBT1) with crucial roles in host defense thus comprising plausible phenotypic targets for treatment of COVID-19.

BackgroundThe microbiome likely plays a role in tuberculosis (TB) pathogenesis. We evaluated the site-of-disease microbiome and predicted metagenome in people with presumptive tuberculous pericarditis, a major cause of mortality, and explored for the first time, the interaction between its association with C-reactive protein (CRP), a potential diagnostic biomarker and the site-of-disease microbiome in extrapulmonary TB. MethodsPeople with effusions requiring diagnostic pericardiocentesis (n=139) provided background sampling controls and pericardial fluid (PF) for 16S rRNA gene sequencing analysed using QIIME2 and PICRUSt2. Blood was collected to measure CRP. ResultsPF from people with definite (dTB, n=91), probable (pTB, n=25), and non- (nTB, n=23) tuberculous pericarditis differed in {beta}-diversity. dTBs were, vs. nTBs, Mycobacterium-, Lacticigenium-, and Kocuria-enriched. Within dTBs, HIV-positives were Mycobacterium-, Bifidobacterium-, Methylobacterium-, and Leptothrix-enriched vs. HIV-negatives and HIV-positive dTBs on ART were Mycobacterium- and Bifidobacterium-depleted vs. those not on ART. Compared to nTBs, dTBs exhibited short-chain fatty acid (SCFA) and mycobacterial metabolism microbial pathway enrichment. People with additional non-pericardial involvement had differentially PF taxa (e.g., Mycobacterium-enrichment and Streptococcus-depletion associated with pulmonary infiltrates). Mycobacterium reads were in 34% (31/91), 8% (2/25) and 17% (4/23) of dTBs, pTBs, and nTBs, respectively. {beta}-diversity differed between patients with CRP above vs. below the median value (Pseudomonas-depleted). There was no correlation between enriched taxa in dTBs and CRP. ConclusionsPF is compositionally distinct based on TB status, HIV (and ART) status and dTBs are enriched in SCFA-associated taxa. The clinical significance of these findings, including mycobacterial reads in nTBs and pTBs, requires evaluation.

Systemic mycobacterial load is associated with outcome in HIV-associated tuberculosis but is poorly defined. We used latent variable modelling to characterise HIV-associated TB mycobacterial load. Mycobacterium tuberculosis detection tests on urine and blood, but not sputum, showed substantial co-variance, and were strongly correlated with host inflammation and mortality.

BackgroundLymphadenitis is the most common extrapulmonary tuberculosis (EPTB) manifestation and a major cause of death. The microbiome is important to human health but uninvestigated in EPTB. We profiled the site-of-disease lymph node microbiome in tuberculosis lymphadenitis (TBL). MethodsFine needle aspiration biopsies (FNABs) were collected from 159 pre-treatment presumptive TBL patients in Cape Town, South Africa. 16S Illumina MiSeq rRNA gene sequencing was done. ResultsWe analysed 89 definite TBLs (dTBLs) and 61 non-TBLs (nTBLs), which had similar -but different {beta}-diversities (p=0.001). Clustering identified five lymphotypes prior to TB status stratification: Mycobacterium-, Prevotella- and Streptococcus-dominant lymphotypes were more frequent in dTBLs whereas a Corynebacterium-dominantlymphotype and a fifth lymphotype (no dominant taxon) were more frequent in nTBLs. When restricted to dTBLs, clustering identified a Mycobacterium-dominant lymphotype with low -diversity and other non-Mycobacterium-dominated lymphotypes (termed Prevotella-Corynebacterium and Prevotella-Streptococcus). The Mycobacterium dTBL lymphotype was associated with HIV-positivity and clinical features characteristic of severe lymphadenitis (e.g., node size). dTBL microbial communities were enriched with potentially proinflammatory microbial short chain fatty acid metabolic pathways (propanoate, butanoate) vs. those in nTBLs. 11% (7/61) of nTBLs had Mycobacterium reads. ConclusionsTBL at the site-of-disease is not microbially homogenous and distinct microbial community clusters exist that are associated with different immunomodulatory potentials and clinical characteristics. Non-Mycobacterium-dominated dTBL lymphotypes, which contain taxa potentially targeted by TB treatment, represent less severe potentially earlier stage disease. These investigations lay foundations for studying the microbiomes role in lymphatic TB and the long-term clinical significance of lymphotypes requires prospective evaluation.

BackgroundStreptococcus pneumoniae (S.pn) is the most prevalent causal bacterial pathogen in community-acquired pneumonia. Despite appropriate antimicrobial therapy, pneumococcal pneumonia can progress to acute respiratory distress syndrome where actual therapies are mainly supportive, and the discovery of new molecular targets is needed. ObjectiveTo investigate the role of IGF1R (Insulin-like Growth Factor 1 Receptor) in pneumococcal pneumonia. MethodsIgf1r-deficient (UBC-CreERT2; Igf1rfl/fl) and control (Igf1rfl/fl) mice were infected with 5x106 S.pn (PN36) or PBS (sham infected). Mice were sacrificed 48 h after infection. Pulmonary permeability, local inflammatory response, and pulmonary and extra-pulmonary bacterial loads were analyzed. Further, IGF1R protein expression was determined in human lung tissue after S.pn infection and IGF1 and IGF1R levels were determined serum of pneumonia patients. ResultsIn patients and mice infected with S.pn, IGF1 signaling was significantly altered. Igf1r-deficient mice had significantly increased pulmonary permeability after infection with increased pulmonary inflammatory cytokine levels, while inflammatory cell recruitment was not altered compared to infected Igf1rfl/fl control animals. Pulmonary bacterial load was significantly higher in Igf1r-deficient mice, and histological analysis confirmed increased alveolar edema and necrosis compared to infected Igf1rfl/fl control and sham-infected mice. Ex vivo, S.pn caused a decrease in IGF1R protein expression in human lung tissue. ConclusionOur results demonstrate a significant regulation of IGF1R in ex-vivo infected human lung tissue and in serum of S.pn pneumonia patients. Moreover, pneumonia severity was increased in Igf1r-deficient mice upon S.pn infection compared to Igf1rfl/fl control mice, suggesting that IGF1R plays a protective role in pneumococcal pneumonia.

Chronic obstructive pulmonary disease (COPD) is one of the major causes of disability and death worldwide and a significant risk factor for respiratory infections. Rhinoviral infections are the most common trigger of COPD exacerbations which lead to a worsening of disease symptoms, decline in lung function and increased mortality. The lack of suitable disease models to study the relevant cellular and molecular mechanism hinders the discovery of novel medicines that prevent disease progression in exacerbating COPD patients. We used quantitative multi-color imaging of COPD and control patient derived human precision-cut lung slices (hPCLS) to study the impact of rhinovirus infection on the structure and function of the small airway epithelium. Data analysis highlighted that COPD-derived hPCLS have a higher cellular density and basal cell hyperplasia, more unciliated airway surface areas with mucus overproduction, and shorter cilia length compared to control hPCLS. In response to rhinovirus 16 infection, COPD-derived hPCLS secreted higher amounts of pro-inflammatory cytokines and displayed decreased epithelial integrity and reduced airway ciliation. Finally, treatment with a selective PI3K{delta} inhibitor reduced secretion of rhinovirus-induced cytokines and ameliorated rhinovirus-induced damage to COPD small airway epithelia. Thus, these data demonstrate the potential of quantitative imaging to assess complex airway functions in a patient-derived lung tissue model system, and indicate that targeting PI3K{delta} might be a promising therapeutic opportunity to limit rhinovirus-induced airway damage in exacerbating COPD patients. SummaryPI3K{delta} inhibition reduces rhinovirus-mediated damage of small airway epithelia from chronic obstructive pulmonary disease (COPD) patients

RationaleIdentification and validation of circulating biomarkers for lung function decline in COPD remains an unmet need. ObjectiveIdentify prognostic and dynamic plasma protein biomarkers of COPD progression. MethodsWe measured plasma proteins using SomaScan from two COPD-enriched cohorts, the Subpopulations and Intermediate Outcomes Measures in COPD Study (SPIROMICS) and Genetic Epidemiology of COPD (COPDGene), and one population-based cohort, Multi-Ethnic Study of Atherosclerosis (MESA) Lung. Using SPIROMICS as a discovery cohort, linear mixed models identified baseline proteins that predicted future change in FEV1 (prognostic model) and proteins whose expression changed with change in lung function (dynamic model). Findings were replicated in COPDGene and MESA-Lung. Using the COPD-enriched cohorts, Gene Set Enrichment Analysis (GSEA) identified proteins shared between COPDGene and SPIROMICS. Metascape identified significant associated pathways. Measurements and Main ResultsThe prognostic model found 7 significant proteins in common (p < 0.05) among all 3 cohorts. After applying false discovery rate (adjusted p < 0.2), leptin remained significant in all three cohorts and growth hormone receptor remained significant in the two COPD cohorts. Elevated baseline levels of leptin and growth hormone receptor were associated with slower rate of decline in FEV1. Twelve proteins were nominally but not FDR significant in the dynamic model and all were distinct from the prognostic model. Metascape identified several immune related pathways unique to prognostic and dynamic proteins. ConclusionWe identified leptin as the most reproducible COPD progression biomarker. The difference between prognostic and dynamic proteins suggests disease activity signatures may be different from prognosis signatures.

BackgroundWe aim to study the source of circulating immune cells expressing a 50-gene signature predictive of COVID-19 and IPF mortality. MethodsWhole blood and Peripheral Blood Mononuclear cells (PBMC) were obtained from 231 subjects with COVID-19, post-COVID-19-ILD, IPF and controls. We measured the 50-gene signature (nCounter, Nanostring), interleukin 6 (IL6), interferon {gamma}-induced protein (IP10), secreted phosphoprotein 1 (SPP1) and transforming growth factor beta (TGF-{beta}) by Luminex. PCR was used to validate COVID-19 endotypes. For single-cell RNA sequencing (scRNA-seq) we used Chromium Controller (10X Genomics). For analysis we used the Scoring Algorithm of Molecular Subphenotypes (SAMS), Cell Ranger, Seurat, Propeller, Kaplan-Meier curves, CoxPH models, Two-way ANOVA, T-test, and Fishers exact. ResultsWe identified three genomic risk profiles based on the 50-gene signature, and a subset of seven genes, associated with low, intermediate, or high-risk of mortality in COVID-19 with significant differences in IL6, IP10, SPP1 and TGF{beta}-1. scRNA-seq identified Monocytic-Myeloid-Derived Suppressive cells (M-MDSCs) expressing CD14+HLA DRlowCD163+ and high levels of the 7-gene signature (7Gene-M-MDSC) in COVID-19. These cells were not observed in post-COVID-19-ILD or IPF. The 43-gene signature was mostly expressed in CD4 T and CD8 T cell subsets. Increased expression of the 43 gene signature was seen in T cell subsets from survivors with post-COVID-19-ILD. The expression of these genes remained low in IPF. ConclusionA 50-gene, high-risk profile in COVID-19 is characterized by a genomic imbalance in monocyte and T-cell subsets that reverses in survivors with post-COVID-19 Interstitial Lung Disease

BackgroundPDLIM2, a PDZ-LIM domain-containing protein expressed highest in the lung and immune cells, serves as a unique tumor suppressor and immune modulator, mainly by turning off the activation of the master transcription factors NF-{kappa}B and STAT3. While its role in cancer is established, the involvement of PDLIM2 in viral infection remains unclear. ResultsHere, we analyzed public gene expression data of blood leukocytes, bronchoalveolar lavage cells, and lung tissues from uninfected healthy humans and those infected with the respiratory virus SARS-CoV-2 or influenza. We found that PDLIM2 expression was repressed by viral infection, and notably, this repression correlated with the severity of infectious diseases. Consistently, the expression level of PDLIM2 was negatively associated with NF-{kappa}B and STAT3 activity across a diverse range of cell types, such as macrophages, monocytes, neutrophils, T cells, alveolar type 1 and 2 epithelial cells, airway epithelial cells, and fibroblasts. Accordingly, cells with low PDLIM2 expression exhibited aberrant activation of signaling pathways essential for cellular functions and immune responses. ConclusionsThese findings highlight PDLIM2 repression as a common mechanism underlying human viral infectious diseases and suggest PDLIM2 as a potential biomarker and therapeutic target for disease prognosis, prevention, and treatment.

Non-sputum-based biomarkers for early diagnosis of TB disease are urgently needed to control transmission and achieve the World Health Organizations goals of ending TB. We previously identified a 12-marker plasma protein signature associated with TB disease severity. In this study we assessed the signatures performance in identifying TB disease in independent Swedish and Italian cohorts, including individuals with TB infection and other respiratory diseases (total n=317 samples from 273 donors). We condensed the 12 proteins to smaller 6 (CDCP1, VEGFA, IFN-{gamma}, CXCL9, IL6 and MCP-3) and 4 (CDCP1, VEGFA, IFN-{gamma}, CXCL9)-protein signatures which remained highly enriched and even improved accuracy when compared with ten other published protein signatures for TB disease. Sensitivity in TB disease compared with TB-infection was 89% in the entire cohort and 97% in the Italian cohort, with specificity fixed at 70%. These signatures merit further evaluation as clinically relevant markers for a non-sputum-based test for TB disease.

Following SARS-CoV-2 Omicron BA.1, subsequent Omicron sub-lineages have continued to emerge, challenging the development of intervention and prevention strategies, including monoclonal antibodies and vaccines. To better understand the pathogenic effects caused by Omicron BA.5 infection, we developed a mouse-adapted virus with overt disease burden in BALB/c mice. Acute disease was characterized by significant weight loss and lung dysfunction following high-dose challenges. In survivor animals that were followed through 107 days post-infection, subpleural fibrosis with associated tertiary lymphoid structures was noted. Serum from these mice demonstrated potent neutralization against BA.5, with substantially reduced neutralization titers against early epidemic, zoonotic, and more recent contemporary XBB.1.5 variants. Intervention with pre-clinical monoclonal antibodies revealed that robust protection from BA.5-induced lung disease was possible after prophylactic administration. Together, this model enables the investigation of therapeutic approaches for both acute and post-acute sequelae of COVID-19. ImportanceIn order to best combat the evolving landscape of SARS-CoV-2 variants of interest and variants of concern the development of effective small animal models is of critical importance. Herein, we describe the development of a model system in BALB/c mice to study the effects of SARS-CoV-2 BA.5 in both acute and chronic disease manifestations. Intriguingly, we determined that fibrotic lung disease with tertiary lymphoid structures was a prominent feature in the lungs of mice that survived through the acute phase of infection. This is a prominent concern in human patients that survive the initial infection insult. As such, and most critically, the model system presented here provides researchers with an effective pathway in which long COVID manifestations and potential interventions can be studied.

Prolonged shedding of infectious SARS-CoV-2 has recently been reported in a number of immunosuppressed individuals with COVID-19. Here, we describe the detection of high levels of replication-competent SARS-CoV-2 in specimens taken from the respiratory tract of a B-cell depleted patient up to 154 days after initial COVID-19 diagnosis concomitant with the development of high mutation rate. In this patient, a total of 11 nonsynonymous mutations were detected in addition to the Y144 deletion in the spike protein of SARS-CoV-2. Virus evolution studies revealed a dramatic diversification in viral population coinciding with treatment with convalescent plasma and clinical respiratory deterioration. Our findings highlight the urgent need for continuous real-time surveillance of genetic changes of SARS-CoV-2 adaptation alongside immunological investigations in patients with severely compromised humoral responses who may shed infectious virus over prolonged periods of time.

BackgroundPost-viral diseases, including post-COVID-19 syndrome (PCS) and myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), cause substantial long-term morbidity. Persistent cardiovascular (CV) risk after acute infection highlights the need for accessible tools to quantify microvascular health. MethodsAll Eyes on PCS is a prospective, observational study investigating the retinal microcirculation using retinal vessel analysis (RVA). We compared RVA parameters in 102 PCS patients with 204 age- and sex-matched healthy controls (HC, matched from n = 303). Secondary matched analyses included never infected controls (NI, n = 96), recovered individuals (n = 102), PCS patients, and ME/CFS patients (n = 62). Laboratory variables, circulating markers of endothelial dysfunction (ED) and inflammation were compared between cohorts and their associations with RVA parameters were examined. ResultsCompared with HC, PCS patients showed reduced venular flicker-induced dilation (3.7 {+/-} 2.2% vs. 4.5 {+/-} 2.7%, p = 0.005), narrow retinal arterioles (CRAE, 178.3 {+/-} 15.5 {micro}m vs. 183.3 {+/-} 15.9 {micro}m, p = 0.009), and lower arteriolar-to-venular ratio (0.83 {+/-} 0.06 vs. 0.86 {+/-} 0.07, p = 0.004). Findings persisted after adjustment for CV factors and remained evident in an extended secondary matched analysis across NI, recovered, and PCS patients. ME/CFS patients showed the most pronounced alterations. PCS severity correlated with lower AVR (r = -0.21, p = 0.037) and reduced arteriolar FID (r = -0.21, p = 0.039), particularly for neurocognitive symptoms. IL-6, ICAM-1 and VCAM-1 were elevated in PCS and ME/CFS and lower AVR correlated with inflammatory and iron-related markers (all adjusted p < 0.01). A combined model discriminated ME/CFS patients with good accuracy (AUC = 0.80). ConclusionsPCS is associated with persistent ED, most pronounced in ME/CFS patients and linked to symptom severity and ongoing inflammation. RVA may provide a noninvasive, readout of ED in post-viral syndromes. Trial RegistrationThe All Eyes on PCS Study has previously been registered at ClinicalTrials.gov (NCT05635552). Novelty and SignificanceO_ST_ABSWhat is known?C_ST_ABS- PCS and ME/CFS are associated with persistent endothelial dysfunction and increased long-term cardiovascular risk. - Neurocognitive symptoms in post-viral syndromes have been linked to impaired neurovascular coupling. - Retinal vessel analysis provides a validated, non-invasive readout of systemic and cerebral microvascular health. What new information does this article contribute?- PCS is characterized by persistent functional and structural retinal microvascular dysfunction - Retinal endothelial dysfunction scales continuously with post-viral disease severity and is most pronounced in patients fulfilling ME/CFS criteria. - Retinal microvascular alterations are linked to inflammatory-endothelial activation and iron dysregulation, identifying a biologically coherent vascular phenotype. This study provides the first comprehensive human in vivo assessment of retinal microvascular structure and function across the full post-COVID-19 spectrum, from never infected controls to recovered individuals, PCS patients, and those fulfilling ME/CFS criteria. Using retinal vessel analysis as a surrogate of neurovascular and endothelial function, we demonstrate that endothelial dysfunction persists in patients with ongoing post-viral symptomatology. Retinal venular flicker-induced dilation, arteriolar caliber, and autoregulatory capacity decline progressively with increasing clinical severity, indicating a dose-response relationship between microvascular injury and post-infectious disease burden. Importantly, these vascular alterations are linked to sustained inflammatory and endothelial activation and to disturbances in iron homeostasis, indicating an inflammatory-endothelial axis rather than isolated cardiovascular risk. By integrating microvascular phenotyping with symptom profiles and circulating biomarkers, this work identifies retinal endothelial dysfunction as a mechanistically informative and clinically accessible marker of post-viral disease severity. These findings advance understanding of post-infectious vascular pathology and provide a translational framework for biological stratification and risk assessment in PCS and ME/CFS.

BackgroundBronchoalveolar lavage (BAL) single-cell RNA sequencing (scRNA-seq) offers rich insights into pulmonary immune dynamics, yet consistent cell-type annotation remains elusive. Existing methods often rely on a single reference, risking inconsistency and domain shift across datasets. A BAL-specific, high-resolution annotation framework is critically needed. MethodsWe developed BAL-EA (BAL Ensemble Annotation), a BAL-centric automated annotation framework that integrates robust, cross-study marker discovery with ensemble machine learning. BAL-EA harmonizes BAL cell identities into a three-tier taxonomy (11 major lineages, 13 refined classes, 21 fine-grained subtypes) compatible with the Human Lung Cell Atlas (HLCA) while capturing lavage-enriched biology. Marker catalogues were derived via reproducibility-guided differential expression across at least 10 independent sub-studies, ensuring resilience to dataset-specific bias. Comparative benchmarking was performed against six leading annotation tools using independent BAL datasets. ResultsWe assembled the largest BAL scRNA-seq atlas to date, integrating more than 347,333 lung cells from HLCA, multiple public BAL datasets, and the largest inhouse BAL cohort ever reported (241,924 cells from 30 individuals). BAL-EA outperformed existing annotation tools, achieving balanced macro-F1 scores over 0.95 for key lineages such as alveolar macrophages (AM), non-alveolar macrophages, and epithelial cells. Application to Chronic Obstructive Pulmonary Disease (COPD) BAL samples revealed reproducible disease-associated shifts, including increased neutrophils and CCL2-positive macrophages alongside reduced AM in COPD patients, findings validated in independent COVID-19 BAL datasets. The released atlas includes harmonized multi-resolution annotations, robust marker panels, pretrained models. ConclusionsThis work contributes the most comprehensive BAL scRNA-seq atlas, introduces a novel BAL-specific annotation framework (BAL-EA), standardizes BAL taxonomy at three resolutions, and provides rigorously validated marker gene resources. Together, these advances deliver a powerful reference for reproducible BAL scRNA-seq analysis and lay the foundation for clinical and translational applications in respiratory disease research.

Cancer-associated fibroblasts (CAFs) are the dominant cell type in the stroma of solid organ cancers, including non-small cell lung cancer (NSCLC). Fibroblast heterogeneity is widely recognised in many cancers, with subpopulations of CAFs being identified and potentially being indicative of prognosis and treatment efficacy. Here, the subtypes displayed by CAFs isolated from human NSCLC resections are initially identified by flow cytometry, using the markers FAP, CD29, SMA, PDPN, CD90, FSP-1 and PDGFR{beta}, showing five distinct subpopulations, CAF-S1-S5. Our findings show that when comparing fibroblasts from tumour tissue with that from adjacent lung tissue, CAF-S2 and CAF-S3 are found in the normal tissue and marker expression suggests a less activated phenotype whereas CAF-S1, CAF-S4 and CAF-S5 are predominantly found in the tumour tissue and are positive for a combination of markers of fibroblast activation. We focus on these subtypes most associated with fibroblast activation, primarily focussing on a previously unreported CAF-S5 subtype, and comparing to the previously identified CAF-S1. Both these subsets express FAP and PDPN as markers of fibroblast activation, but CAF-S5 lacks expression of the common activation marker SMA. The spatial relevance of these subtypes in a cohort of 163 NSCLC patients was then investigated by multiplex immunofluorescence on a tumour micro-array of patient samples, revealing CAF-S5 are found further from tumour regions than CAF-S1. To understand the functional role of CAF-S5, scRNA sequencing data was used to compare the subset to the previously identified CAF-S1, finding that CAF-S5 displays an inflammatory phenotype, whereas CAF-S1 displays a contractile phenotype. We demonstrate that presence of either the CAF-S1 or CAF-S5 subtype is correlated to worse survival outcome in NSCLC, highlighting the importance of the identification of CAF subtypes in NSCLC.