EBioMedicine最新文献

Background: Hepatitis C virus (HCV) remains a major global health challenge, largely due to the absence of robust animal models that recapitulate this disease, hindering mechanistic studies and vaccine development. This study employed tree shrews to determine the molecular profiles of distinct liver cell populations following HCV infection.

Methods: Tree shrews received intrahepatic injections of the HCV JFH1 strain and were analysed at two timepoints: 1 week post-inoculation (acute) and 111 weeks post-inoculation (long-term). Viral load was assessed up to 30 weeks. Liver pathology was assessed via haematoxylin and eosin (H&E) staining. Single-cell transcriptomic profiling was performed on liver tissues, while tree shrew primary hepatocytes and ITH6 hepatic cells, as well as human Huh7 cells, were used to characterise cellular changes following HCV infection.

Findings: Sixteen major cell types were identified in 157,298 liver cells across HCV-inoculated and control tree shrews. Acute inoculation triggered widespread induction of interferon-stimulated genes (ISGs) across all cell types, including the periportal ISG^high hepatocyte subcluster, and concurrent reduction in metabolic gene expression in hepatocytes in vivo. Impaired glucose metabolism, as confirmed in HCV-exposed ITH6 cells, likely contributed to this metabolic shift. Erythroblasts were exclusively detected during acute inoculation and exhibited enhanced intercellular communication signatures. Among neutrophils, three distinct subclusters were identified, one of which displayed elevated expression of neutrophil extracellular trap (NET) markers and enhanced NET formation in inoculated livers.

Interpretation: This study provides a comprehensive single-cell transcriptomic landscape of HCV-inoculated tree shrew livers. These findings underscore the use of the tree shrew model for advancing mechanistic understanding of HCV pathogenesis, as well as its relevance for therapeutic and vaccine development.

Funding: This work was supported by grants from National Natural Science Foundation of China (U1902215, U25A20646), National Key Research and Development Plan Program (2022YFF0710900), Key Project of the CAS "Light of West China" Program (xbzg-zdsys-202302), and Yunnan Province (202305AH340006, 202001AS070023).

Background: Sjögren's Disease (SjD) is a systemic autoimmune disorder characterised by exocrine gland dysfunction and immune infiltration. However, the spatial cellular architecture and metabolic-immune crosstalk underlying glandular pathology in SjD remain unclear.

Methods: We performed spatial transcriptomics on SjD salivary glands (SGs) and conducted integrative analyses with single-cell RNA sequencing to delineate disease-specific transcriptomic alterations, followed by validation in an independent cohort. Key findings were verified via immunofluorescence, immunohistochemistry, and function assays on cells.

Findings: Spatial clustering revealed distinct perturbations in SjD. We identified a pathogenic CCL2^high fibroblast-ACKR1^high endothelial cell axis that co-localised in lymphoid foci and correlated with immune infiltration and disease activity. Chemokine-receptor axes were associated with immune infiltration, with endothelial ACKR1 facilitating inflammatory niche organisation. Compartmentalised immune-stroma niches exhibited upregulated phospholipid, glycerophospholipid and phosphatidylinositol metabolism in lymphoid foci, correlating with B/T-cell activation and interferon responses. Key metabolic regulators (PIK3CD, PIK3CG, PIKFYVE, and PLCG2) were elevated in SjD, associated with CD45⁺ cell abundance in SGs, and exhibited diagnostic potential. Conversely, epithelial cells showed suppressed glycerolipid metabolism and decreased MGLL expression, linked to enhanced antigen presentation. Inhibiting monoacylglycerol lipase (encoded by MGLL) upregulates MHC in A253 cells, while interferon-γ suppresses MGLL expression.

Interpretation: Our study elucidates spatially organised metabolic-immune networks in SjD, implicating lipid metabolism in immune activation and epithelial metabolic reprogramming in secretory dysfunction, nominating promising therapeutic targets.

Funding: National Natural Science Foundation of China (82104484,32301084), Joint funding from schools (colleges) and enterprises in Guangzhou (2025A03J3203, 2024A03J0987), Natural Science Foundation of Guangdong Province (2023A1515012790), Guangdong Provincial Enterprise Joint Fund (2022A1515220003), and Sun Yat-sen University (P02523).

Background: Epilepsy is a heterogeneous syndrome. Personalised localisation of epileptogenic zone (EZ) is critical for diagnosis and treatment of drug-resistant focal epilepsy. Multichannel stereoelectroencephalography (SEEG) monitoring acquired over a period of two to three weeks was collected in different patients, resulting in comprehensive epileptogenic information and terabytes of high dimensional data. Consequently, there is a need for high-throughput data analytical methods to enable data-driven, personalised seizure detection and EZ localisation.

Methods: Here, a seizure detection and EZ localisation AI system - SEEGformer is proposed, by utilising SEEG data from 61 patients acquired across two centres and three cohorts capturing tens of thousands of abnormal discharges and around ten seizures per person on average. SEEGformer employs a parallel transformer architecture to analyse multiple representations of multichannel SEEG signals, including the real part, imaginary part, and amplitude of the analytic signal after Fourier transform. The MRI information was encoded in SEEGformer to construct the structural dependence of the brain areas. Inter-channel dependencies and interactions were captured for seizure detection. A cross-channel attention mechanism computed the epileptogenic risk score for each channel to localise EZ using ictal SEEG data. Each patient's SEEG data was used to train and validate their individual-specific SEEGformer model.

Findings: In three clinical cohorts, SEEGformer achieved an average AUROC of 0.937 (95% CI, 0.922-0.950) for seizure detection and 0.798 (95% CI, 0.749-0.847) for EZ localisation. Localisation performance surpassed state-of-the-art methods by over 5%. SEEGformer further revealed distinct phase synchronisation patterns in dynamically evolving epileptogenic zone networks, with a significance level of P < 0.0001.

Interpretation: Due to its high interpretability and visualisation capabilities, SEEGformer can enhance clinical decision-making by providing an objective, data-driven reference to optimise epileptogenic zone delineation and surgical strategy development. Currently, the improved SEEGformer is being developed to construct a dedicated SEEG atlas for epilepsy.

Funding: This study was funded by Natural Science Foundation of Shanghai (25ZR1401179), the National Key Research and Development Program of China (2022YFB4702702), the Sci-Tech Innovation 2030-Major Project of Brain Science and Brain-inspired Intelligence Technology (2021ZD0200600), Beijing Municipal Public Welfare Development and Reform Pilot Project for Medical Research Institutes (JYY2023-8), and National Key Research and Development Program of China (2024YFC3044700).

Background: Treatment decisions in patients with unresectable colorectal liver metastases (CRLM) are largely guided by radiological response to induction systemic therapy. However, radiological assessment alone provides an imprecise estimate of underlying tumour biology or treatment response. Circulating tumour DNA (ctDNA) is an emerging biomarker that can support clinical decision-making. This study evaluated the independent prognostic value of radiological tumour burden and DELFI-TF, a tumour tissue- and mutation-independent cell-free DNA (cfDNA) fragmentome-based ctDNA assay.

Methods: We analysed 202 plasma samples and CT scans collected at baseline and following induction systemic therapy from 101 patients with unresectable, liver-limited CRC enrolled in the phase-III CAIRO5 trial (NCT02162563), treated with FOLFOX/FOLFIRI plus bevacizumab. Total tumour volume (TTV) was centrally quantified via semi-automated segmentation of liver metastases. ctDNA was measured using the DELFI-TF score. Associations with overall survival (OS) and early recurrence were evaluated using multivariable Cox regression models.

Findings: At baseline, TTV (median = 139 mL, IQR = 23-497 mL) strongly correlated with DELFI-TF (median = 0.29, IQR = 0.13-0.41; Spearman's ρ = 0.70). DELFI-TF showed a more pronounced reduction than TTV on-treatment (-97.6% vs -49.9%). Baseline levels and on-treatment changes of DELFI-TF (P = 0.001; P = 0.012) and TTV (P = 0.002; P = 0.002) were independently associated with OS in the multivariable model; their combination improved prognostic performance (Uno's C-statistic 0.78 vs 0.73; P = 0.036). Baseline (P = 0.016) and on-treatment DELFI-TF (P = 0.001) also predicted early recurrence after local therapy.

Interpretation: Following further validation, integrating cfDNA fragmentome-based testing with radiological tumour volume may provide complementary and clinically meaningful insights for prognostication and treatment response in patients with unresectable CRLM. This exploratory study supports a multimodal biomarker approach to guide personalised treatment strategies.

Funding: German Research Foundation (DFG, 513004649), Heidelberg Medical Faculty, Dutch Cancer Society/KWF Kankerbestrijding (10438), PPP Allowance via Health ∼ Holland (LSHM22027), Dr. Miriam and Sheldon G. Adelson Medical Research Foundation, Stand Up To Cancer (SU2C)in-Time Lung Cancer Interception Dream Team Grant, SU2C-Dutch Cancer Society International Translational Cancer Research Dream Team Grant (SU2C-AACR-DT1415), Gray Foundation, Commonwealth Foundation, Cole Foundation, Delfi Diagnostics (research grant), US National Institutes of Health (CA121113, CA233259, CA271896).

Background: Sex-based differences in morbidity and mortality in pulmonary hypertension (PH) are underexplored, yet understanding these differences is vital for improving clinical management. This study investigates the influence of sex on survival of patients with PH in dependency of various disease conditions.

Methods: The PVRI GoDeep meta-registry integrates data from international PH registries, of which we analysed 21,123 incident hemodynamically fully characterised patients with PH. Survival analyses employed Kaplan-Meier and Cox proportional hazards models, adjusted for confounders and subjected to sensitivity analyses.

Findings: Male patients consistently showed significantly higher mortality than females across the overall PH population (hazard ratio 1.36 [1.23, 1.50] after adjustment) and within PAH and non-PAH groups. These sex differences in survival persisted regardless of P(A)H severities, age and obesity, cardiovascular diseases, and PAH-specific therapies. The male survival disadvantage was noted across low-, intermediate-, and high-risk groups of the ESC/ERS 2022, REVEAL lite 2, and COMPERA 4-strata scores, but not the REVEAL 2.0 risk score, which incorporates male sex as non-modifiable factor. Stratification by race revealed that male sex was associated with worse survival in White patients, but not in Black or Asian patients with PH.

Interpretation: Male patients with PH exhibit significantly higher mortality risks than females across both PAH and non-PAH PH groups. This disparity persists regardless of PH severity, underlying cause, age, obesity, comorbidities, or treatment status, though race might modify the observed risk difference. These insights provide new avenues for investigating underlying mechanisms and suggest including male sex as an independent factor in clinical risk assessment tools.

Funding: This work is funded by the Pulmonary Vascular Research Institute (PVRI) and the Cardiovascular Medical Research and Education Fund (CMREF), NIH.

Background: Procalcitonin (PCT) is a biomarker used to differentiate between viral and bacterial infections, though the underlying mechanisms are not yet fully understood. This study aimed to identify genetic variants associated with plasma PCT concentrations and explore the associations of genetically predicted PCT with a wide range of disease related traits in a PheWAS.

Methods: We conducted GWAS and meta-analysis using data from the MDCS (n = 4007), MPP (n = 5097), and PREVEND (n = 3344) cohorts. We used fine-mapping to prioritise likely causal variants and explored regulatory effects using eQTL data, summary-data-based Mendelian randomisation (SMR) and colocalisation. To validate the PCT findings, we conducted multi-trait analysis of GWAS (MTAG) combining our results with CALCA data from a large pQTL study. The polygenic risk score (PRS) for PCT was calculated in the UK Biobank (n = 457,418) based on the GWAS summary data, and associations between the PRS and 179 traits were assessed in a PheWAS.

Findings: We identified four independent significant SNPs in three loci associated with plasma PCT: CALCB (rs7119706, rs10832337), PBX4 (rs17217098), and PRDM15 (rs7277773). Fine-mapping prioritised 18 likely causal variants, including rs7119706 (near CALCB) and rs16930609 (mapped to CYP2R1) at the chromosome 11 locus. Our eQTL lookup identified significant results for 13 genes, but SMR and colocalisation analyses did not support their potentially causal effects on plasma PCT. The MTAG identified 28 additional significant SNPs across 14 loci. The PheWAS results revealed that PRS was associated with calcium metabolism-related traits, including calcium concentrations (p = 7.0 × 10^-5), vitamin D concentrations (p = 2.0 × 10^-219), and bone fractures (p = 6.5 × 10^-4); metabolic traits, cardiovascular, renal, and liver function-related traits, and inflammation and immune-related traits.

Interpretation: Our findings suggest that genetically predicted PCT is associated with multiple pathways including calcium metabolism and immune function, and has potential clinical implications for bone health, kidney function, and type 2 diabetes.

Funding: China Scholarship Council (File no. 202006210041 to WZ and 201906010319 to SW, respectively).

Background: Diagnostic assays have been introduced to diagnose human papillomavirus (HPV)-driven oropharyngeal cancer (HPV-OPC), including those identifying HPV16-L1 antibodies. This study aims to evaluate the diagnostic accuracy of an HPV16-L1 antibody rapid test for HPV-OPC, and its performance in individuals likely to have HPV16-L1 antibodies from causes other than HPV-OPC.

Methods: Serum samples (n = 235) from three study populations were tested using a CE-certified serological HPV16-L1 antibody rapid test (Prevo-Check®) at the German National Reference Center for Papillomaviruses. Laboratory personnel were blinded to participant characteristics and followed the manufacturer's instructions. The three study populations consisted of: (1) patients with HPV16-positive or -negative OPC (n = 83), (2) bivalent (HPV16/18) vaccine recipients (n = 50), with paired baseline and one-month post-third-dose serum samples, and (3) naturally HPV16 infected young adults (n = 26), with paired serum samples before and after HPV16 seroconversion.

Findings: In the study population with patients with OPC, the sensitivity of the HPV16-L1 antibody rapid test to detect HPV-OPC was 25.0% (95% CI: 13.6, 39.6), and its specificity was 97.1% (95% CI: 85.1, 99.9). The positive predictive value was 92.3% (95% CI: 64.0, 99.8) and negative predictive value 48.6% (95% CI: 36.4, 60.8). In the other study populations, the test was negative for all pre-vaccination samples, and all samples collected before incident natural HPV16 infection. Nearly all post-vaccination samples (98.0%), and one-third of the samples after natural HPV16 infection (34.6%) tested positive in the HPV16-L1 antibody rapid test.

Interpretation: The HPV16-L1 antibody test has low diagnostic accuracy and cannot reliably distinguish different sources of HPV16-L1 antibodies. Therefore, this type of assays is not suitable for screening and detection of HPV16-driven OPC.

Funding: This study is supported by the Ministry of Research, Technology and Space (BMFTR) core bvfunding provided to DKFZ. The NRC for Papilloma- and Polyomaviruses is supported by the Ministry of Health (BMG, grant no. 1369-401).

Background: Amyotrophic lateral sclerosis (ALS) is a severe motor neuron disease, with highly diverse survival time. However, genetic and epigenetic factors influencing ALS survival across diverse populations remain unclear.

Methods: We performed whole-genome sequencing (WGS) and DNA methylome array in blood DNA of patients with ALS. For survival analysis, we used Cox proportional hazards model for genetic variants, DNA methylation (DNAm) of CpG sites or CpG-SNPs in Chinese and Canadian cohorts, followed by meta-analysis. We performed pathway enrichment analysis for candidate genes inferred from DNAm events associated with survival. In paired genome and methylome data, we analysed the effect of the candidate CpG-SNP genotypes on DNAm status.

Findings: Genome-wide cross-population meta-analysis of common variants in 511 patients with ALS showed a suggestive association of CAV1/CAV2 rs117002347 genotypes with survival. Epigenome-wide cross-population meta-analysis in 459 patients revealed that ALS survival was significantly linked to DNAm of 88 CpGs on 40 genes, and highlighted the AMPK and cytoskeleton pathways. Epigenome-wide cross-population meta-analysis of CpG-SNPs in 459 patients identified 8 loci on 4 genes, including BAG6 (cg27014438/rs28732154), which was further validated in another 204 patients with ALS. Moreover, analysis of paired genome/epigenome data (n = 454) indicated that BAG6 rs28732154 genotypes may modulate cg27014438 methylation, which is also a cis-eQTM of BAG6 expression in blood.

Interpretation: Our study identified BAG6 cg27014438 methylation as a potential epigenetic modifier of ALS survival. BAG6 cg27014438 methylation is modulated by rs28732154 genotypes, and linked to BAG6 expression. Our findings extended our understanding of epigenetic modifiers in ALS survival.

Funding: This work was supported by the National Natural Science Foundation of China (82071430, 82371878) (MZ), Shanghai Municipal Natural Science Foundation General Program (22ZR1466400) (MZ), the Fundamental Research Funds for the Central Universities (MZ), the G. Harry Sheppard Memorial Research Fund, and Canadian Consortium on Neurodegeneration in Aging (ER).