Early, intensive dietary intervention may open a therapeutic window for type 2 diabetes (T2D) remission. We conducted a randomized, 2:1 crossover trial in 34 newly diagnosed overweight or obese patients with T2D. Participants were assigned to receive either high-fiber nutritional therapy (HFNT)-a 7-day very-low-calorie, high-fiber diet followed by a 23-day standard diabetes diet-or conventional diabetes treatment (control condition). Each treatment was administered for 90 days before crossover. Compared with the control condition, early HFNT led to greater reductions in HbA1c [-9.45% (-18.04, -4.63) vs 1.44% (-7.73, 3.08); P = 0.010] and fasting plasma glucose [-12.70% (-24.51, -6.01) vs 3.46% (-8.14, 0.94); P = 0.005], while changes in BMI and HOMA-IR were not significant (P > 0.05). Gut microbiome profiling revealed enrichment of short-chain fatty acid-producing taxa (Eubacterium ruminantium group, Blautia, Roseburia, Akkermansia muciniphila, Oscillospira) and depletion of pathogenic genera (Escherichia-Shigella) after HFNT, with compositional shifts correlating with improved glycemic control. Notably, glycemic benefits in participants receiving HFNT first persisted after crossover, whereas participants receiving conventional care first did not achieve full metabolic recovery after switching. These findings suggest that in newly diagnosed T2D, early, fiber-enriched, intermittent energy restriction can induce durable glycemic improvements, potentially mediated by gut microbiota remodeling. This trial highlights a narrow but impactful nutritional intervention window that may alter the trajectory of T2D progression.

BackgroundPatients with active ankylosing spondylitis (AS) exhibit substantial heterogeneity in their clinical responses to tumor necrosis factor alpha inhibitors (TNFi). Consensus clustering, an unsupervised cluster discovery method, may identify AS subgroups with more homogeneous treatment response patterns to adalimumab (ADA), a widely prescribed TNFi.MethodsWe performed longitudinal consensus clustering based on 8 repeated measurements of 10 core response variables in 438 patients with active AS enrolled in a 24-week phase III randomized controlled trial of ADA or its biosimilar, IBI303. Baseline characteristics and important endpoints—including the Assessment of SpondyloArthritis International Society (ASAS)-based and Ankylosing Spondylitis Disease Activity Score Inactive Disease (ASDAS)-based response criteria—were compared between the identified clusters. Predictive models of cluster membership reconstructed from data beyond week 2 were developed and internally validated to facilitate early, prospective identification of the clusters based on baseline and week-2 data.ResultsTwo longitudinal clusters were characterized: a favorable-response cluster (C1, n = 246, 56.2%) and a less favorable-response cluster (C2, n = 192, 43.8%). Compared with C1, C2 was characterized by older age, longer disease duration, and more frequent prior TNFi exposure, despite comparable baseline C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR). For the majority of clinical endpoints except CRP and BASMI, significant divergence emerged as early as week 2 and was sustained through week 24. For instance, C1 achieved significantly higher rates of ASDAS-Inactive Disease (ASDAS-ID) than C2 at week 2 (0.21 [95% CI 0.16, 0.26] vs. 0.01 [95% CI 0.00, 0.02]; Risk Difference [RD]: -0.21 [95% CI -0.26, -0.15], p < 0.001) and week 24 (0.63 [95% CI 0.57, 0.69] vs. 0.14 [95% CI 0.09, 0.18]; RD: -0.49 [95% CI -0.57, -0.42], p < 0.001). A multivariable model incorporating one baseline and eight week-2 variables had an optimism-corrected C-statistic of 0.880 [95% CI 0.859, 0.915] to correctly identify C2.ConclusionsThese observed response trajectories exhibited distinct baseline characteristics and early response divergence at week 2. While these findings provide a hypothesis-generating framework for early patient stratification, their utility for prospective clinical patient triage requires further independent validation.

We report the largest genome-wide association study meta-analysis in ankylosing spondylitis (AS) to date (25,645 cases, 71,224 controls), identifying 27 novel loci and 86 independent genetic associations. Variations in FUT2 (non-secretor status) and ABO (blood group A) increase AS risk, with Mendelian randomisation (MR) linking non-secretor status to increased AS risk from reduced gut carriage of Ruminococcus torques. Associations with three telomerase maintenance genes (TERT, TERC, RTEL1), and MR analysis, suggest increased telomere length causally increases AS susceptibility. Fine-mapping prioritised likely causal variants at multiple loci. Transcriptome- and proteome-wide association studies implicated 644 genes, highlighting immune-related pathways. Lower genetically-determined IL-6 and IL-12, and similar IL-23, levels were found in AS cases, offering a genetic explanation for the failure of IL-6, IL-12, and IL-23 inhibition in AS treatment. Finally, multi-omic analyses showed chromosome 2p15 association acts via reduced B3GNT2 expression. These findings deepen understanding of AS pathogenesis, highlighting new pathways and therapeutic opportunities.

IntroductionPainful diabetic peripheral neuropathy (PDPN) is closely linked to cognitive dysfunction. The gut microbiota plays a pivotal role in the pathophysiology of diabetic neuropathy, but its contribution, along with related metabolites, to PDPN complicated by cognitive impairment remains poorly understood. This study aimed to explore the characteristics of gut microbiota and metabolites in db/db mice with PDPN and concomitant cognitive impairment, and to investigate the underlying mechanisms.MethodsMale homozygous db/db mice and their littermate db/m mice used as the research subjects. Thermal hyperalgesia and mechanical allodynia tests were applied to assess pain phenotypes, while the Morris water maze test was used to evaluate cognitive function. Immunohistochemistry was employed to measure intraepidermal nerve fiber density and nerve fiber markers, and Western blot analysis was used to detect pro-inflammatory cytokine levels. 16S rRNA gene sequencing of the V3-V4 regions was applied to analyze the gut microbiota structure, and LC-MS was used to analyze fecal metabolites.ResultsAt 12 weeks of age, db/db mice exhibited PDPN and cognitive deficits. The gut microbiota composition differed between the two groups, with LEfSe analysis identifying 38 key amplicon sequence variants (ASVs) enriched in db/db mice and 39 ASVs more abundant in db/m mice. Meanwhile, 398 metabolites that were significantly different between the two groups. Bidirectional mediation models indicated that Dl-lactate positively mediated the relationship between specific microbiota (Muribaculaceae (ASV243) and Ruminococcus (ASV149)) and thermal latency. In contrast, polygalic acid negatively mediated the relationship between Muribaculaceae and escape latency, as well as between Ruminococcus and thermal latency. These microbiota and metabolite changes were associated with elevated proinflammatory cytokine levels in the dorsal root ganglion (DRG) and hippocampus, respectively.DiscussionThis study highlights the intricate relationship between gut microbiota, metabolites, and both PDPN and cognitive dysfunction in db/db mice. It also provides insights into potential mechanisms underlying the pathophysiology of these comorbidities, suggesting that modulation of the gut microbiota and its metabolites may offer new therapeutic strategies.

BACKGROUND:Autoreactive B cells play a key role in the pathogenesis of systemic lupus erythematosus (SLE). The aim of this study is to assess the safety of allogeneic chimeric antigen receptor (CAR)-T cells for patients with lupus. This study was registered at ClinicalTrials.gov (NCT05859997). METHODS:In this study, 3 patients with refractory and severe SLE with multi-organ involvement were enrolled. Genetically engineered healthy-donor-derived, CD19-targeting CAR-T cells were infused intravenously at a dose of 1 million cells per kilogram of body weight. The safety indices, including the occurrence of graft-versus-host disease (GvHD), cytokine release syndrome (CRS), and immune effector cell-associated neurotoxicity syndrome (ICANS), were evaluated. The proliferation of CAR+ T cells and the number of peripheral B cells were assessed. The clinical efficacy was also assessed based on the SELENA-SLEDAI, SLEDAI-2K, BILAG, clinical SLE responder index-4 (SRI-4), and DORIS remission index. FINDINGS:Between August 2023 and October 2023, 3 patients with SLE were enrolled and completed a 12-month follow-up. No patient underwent GvHD, CRS, or ICANS, and no severe adverse events were recorded. CAR+ T cells expanded in vivo, peaking at day 14, and then declined. The percentage of B cells in lymphocytes and the absolute circulating B cell counts were profoundly decreased. Patient 1 withdrew from the study at month 1 due to unresolved and severe thrombocytopenia and the need for the addition of an immunosuppressive drug. SELENA-SLEDAI and SLEDAI-2K scores declined, and all the patients reached SRI-4 remission at the last visit. CONCLUSIONS:In patients with severe and refractory SLE, allogeneic CAR-T cell therapy showed profound safety and clinical efficacy for disease remission. FUNDING:82320108010, 31821003, 81930043, 82330055, and U24A20380.

Autoimmune diseases occur when the immune system abnormally attacks the body's normal tissues, causing inflammation and damage. Each disease has unique immune and metabolic dysfunctions during pathogenesis. In rheumatoid arthritis (RA), immune cells have different metabolic patterns and mitochondrial/lysosomal dysfunctions at different disease stages. In systemic lupus erythematosus (SLE), type I interferon (IFN) causes immune cell metabolic dysregulation, linking activation to metabolic shifts that may worsen the disease. In systemic sclerosis (SSc), mitochondrial changes affect fibroblast metabolism and the immune response. Idiopathic inflammatory myopathies (IIMs) patients have mitochondrial and metabolic issues. In primary Sjögren's syndrome (pSS), immune cell metabolism is imbalanced and mitochondrial damage can lead to cell/tissue damage. Metabolic reprogramming links cellular energy needs and immune dysfunctions, causing inflammation, damage, and symptoms in these diseases. It also affects immune cell functions like differentiation, proliferation, and secretion. This review discusses the potential of targeting metabolic pathways to restore immune balance, offering directions for future autoimmune disease research and treatment.

Pogostemon cablin Benth. (P. cablin) is an annual aromatic medicinal plant. In this study, anthers were cultured in vitro during the microspore development stage of P. cablin, inducing somatic embryogenesis. Globular somatic embryos (GSE), heart-shaped somatic embryos, torpedo-shaped somatic embryos, and cotyledonary somatic embryos (CSE) were observed and isolated. Single-cell RNA sequencing was then employed to generate single-cell maps for GSE and CSE. Using reported marker genes, a total of eight cell types were identified. Pseudo-temporal analysis reconstructed the continuous differentiation trajectory of apical meristem cells and epidermal cells. Further investigation identified PcNAC048 as a putative transcription factor that regulates embryonic cell differentiation. Gene expression analysis showed PcNAC048 is expressed in different tissues of P. cablin and responds to abiotic stress. Transgenic studies in Arabidopsis thaliana showed that PcNAC048 can promote lateral root development. Results from yeast one-hybrid and dual luciferase assays showed that PcNAC048 can interact with the promoter of the patchouli alcohol synthase gene (PcPTS) and inhibit its activity. Transient overexpression and virus-induced gene silencing (VIGS) analysis further confirmed that PcNAC048 can negatively regulate the biosynthesis of patchouli alcohol. Overall, this study provides theoretical support for germplasm development and regulation of medicinal compounds in P. cablin. In patchouli (Pogostemon cablin), anther-derived somatic embryos were profiled by single-cell RNA-seq to define eight cell types, identifying PcNAC048 that drives embryonic cell differentiation, promotes lateral root development in Arabidopsis, and negatively regulates patchouli alcohol biosynthesis.

OBJECTIVE:The aim of this study was to explore the functional role of LAMP3-mediated epithelial-mesenchymal transition (EMT) in fibroblast-like synoviocytes (FLSs) in rheumatoid arthritis (RA) patients and to evaluate its potential as a therapeutic target. METHODOLOGY:Changes in EMT and LAMP3 were investigated in the synovial tissue and FLSs of RA patients. In vitro experiments were performed using the EMT inhibitor C19, siRNA, and lentivirus to examine the impact of EMT and LAMP3 on RA-FLSs and the underlying mechanisms involved. Finally, C19 was administered to mice with collagen-induced arthritis (CIA) to validate the therapeutic efficacy of C19 in treating arthritis. RESULTS:Compared with patients with osteoarthritis (OA), RA patients exhibited increased EMT and increased expression of LAMP3 in the synovium. The results from the in vitro experiments demonstrated that inhibiting EMT effectively reduced the excessive proliferation, anti-senescent properties, migration, and invasive behavior of RA-FLSs, as well as the secretion of MMP1, MMP3, and MMP13. Additionally, regulating the expression of LAMP3 not only affected the EMT pathway but also impacted the excessive proliferation and invasive behavior of RA-FLSs. In the CIA model, administration of the EMT inhibitor C19 significantly alleviated the progression of arthritis. CONCLUSION:These findings demonstrate the inhibitory impact of EMT on arthritis and suggest that inhibiting EMT or LAMP3 may be a promising novel therapeutic approach for treating RA.

This study reports the first-in-human application of iPSC-derived CD19/BCMA dual-targeting chimeric antigen receptor-natural killer (CAR-NK) cells (QN-139b) in a patient with severe, diffuse cutaneous systemic sclerosis. The allogeneic product was genetically edited for reduced alloreactivity and improved in vivo performance, with no structural chromosomal abnormalities detected. The treatment led to significant B cell depletion with minimal toxicity, similar to CAR T cell therapy. The patient showed marked clinical improvements during the 6-month follow-up, including reduced autoantibodies and reversed fibrosis, which are resistant to conventional treatments. Single-cell analysis of peripheral blood revealed that the treatment shifted B cells toward more naive phenotypes and eliminated pathogenic B cells. Proteomic studies demonstrated suppression of inflammation and fibrosis, enhanced tissue regeneration, and improved angiogenesis. Pathological evaluation confirmed the elimination of infiltrated lymphocytes from affected skin along with restored skin and microvascular structure. These findings suggest QN-139b is a promising immune-modulatory treatment for severe autoimmune diseases.

Commercial autologous anti-CD19 chimeric antigen receptor-T cell therapies are effective in B cell malignancies and autoimmune diseases but are limited by personalized manufacturing, high costs and the risk from random chimeric antigen receptor insertion into the genome. To overcome these challenges, we developed YTS109, a hypoimmune allogeneic T cell product engineered using CRISPR-Cas9 to knock out TRAC, PD1, HLA-A, HLA-B and CIITA, with a CD19-targeting synthetic TCR and antigen receptor (STAR) precisely integrated into the TRAC locus to enable physiological, TCR-like signaling. As part of a multi-disease cohort trial, this article includes all enrolled five patients with severe, refractory systemic lupus erythematosus (SLE) complicated by lupus nephritis, who received lymphodepletion followed by YTS109 at 3 × 106 STAR⁺ T cells per kg body weight. Primary endpoints were safety and SLE responder index 4 at month (M) 3. Secondary endpoints included clinical remission and quality-of-life outcomes through to M6. YTS109 was well tolerated, with only mild cytokine release syndrome and no graft-versus-host disease. All five patients in the SLE cohort achieved SLE responder index 4 response at M3, which was sustained through to M6. Four of five patients showed a rapid and sustained reduction in SLE disease activity score (mean 31.30-5.35 by M6), while one patient showed a mild refractory flare-up at M6. Quality-of-life improvements were observed across all four instruments in five patients by 6 months after infusion. Renal biopsies further confirmed resolution of inflammation and tissue restoration. These results demonstrate that YTS109 induced immune resetting and clinical remission, including renal structural restoration, potentially offering a promising therapy for refractory SLE with severe lupus nephritis, pending further validation. ClinicalTrials.gov registration: NCT06379646 .

Primary Sjogren's syndrome (pSS) presents as a persistent inflammatory condition marked by a spectrum of symptoms and a limited array of conventional therapeutic interventions. Within Traditional Chinese Medicine (TCM), the Qiju Dihuang Pill (QJDHW) stands as a frequently employed prescription for addressing this syndrome, yet the underlying therapeutic mechanisms remain elusive. Traditional Chinese Medicine Systems Pharmacology (TCMSP) and three disease gene databases, DisGnet, GeneCards, and OMIM, were utilized to establish QJDHW targets and pSS-related gene sets. Cytoscape was used to construct Protein-protein interaction (PPI) and active compound-target networks, followed by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment via the DAVID database. Molecular docking was conducted with AutoDock Vina, and in vitro experiments verified the key findings. A total of 62 overlapping targets were identified. Network analysis revealed quercetin and kaempferol as major active compounds. KEGG enrichment indicated that QJDHW may exert its therapeutic effects by modulating the immune-inflammatory response. Four key targets, namely NFKBIA, IL-6, JUN, and IL-1B, were identified as the central mediators. Molecular docking analysis confirmed their binding affinity with the major active compounds. In vitro assays further confirmed that quercetin and kaempferol suppressed the mRNA expression of key inflammation-related factors, including IL-6, IL-1B, JUN, and NFKB, while reducing IL-6 and IL-1B protein levels and significantly inhibiting the phosphorylation of JUN and NFKB. Collectively, the integration of network pharmacology and experimental validation demonstrated that QJDHW exerts anti-inflammatory effects in treating pSS.

Calcific aortic valve disease (CAVD) is a common disorder associated with substantial morbidity and mortality. Although the gut microbiome has complex associations with cardiovascular disease, its variation across the calcification spectrum in CAVD remains poorly defined. We profiled aortic-valve transcriptomes from 31 patients spanning graded calcification and paired these with matched stool microbiome profiles. We identified subtle yet widespread transcriptional changes in mild CAVD (m-CAVD), consistent with a progressive relationship between calcification burden and gene-expression remodeling. At the community level, the gut microbiome in m-CAVD exhibited an intermediate configuration between non- and higher-calcification profiles, suggesting an early shift in the gut ecosystem along the disease continuum. At the genus level, we identified 11 taxa associated with stage; notably, Anaerococcus increased with calcification burden, whereas Rheinheimera declined across stages. These results refine the pathophysiology landscape of CAVD by connecting stage-dependent valvular transcriptional changes with coordinated shifts in the gut microbiome and indicate that early, microbiome-targeted interventions may be promising. IMPORTANCE:Calcific aortic valve disease is a common valvular heart disease. Due to the difficulty in sampling arterial calcified tissues, research on the interaction between their gene expression and the gut has been limited. In this study, by analyzing the transcriptional profiles of calcified aortic valve tissues from patients with different levels of calcification and the characteristics of their corresponding gut microbiota, we identified consistent features between lesion gene expression and gut microbiota variation. This provides important evidence for the association between the gut microbiota and disease development stages, offering a new perspective for understanding disease progression and early intervention.

Pseudomonas protegens is an important biocontrol agent with the ability to suppress plant pathogens and promote plant growth. P. protegens’ ability to endure hyperosmotic stress is crucial to its effectiveness as a biocontrol agent. This study elucidated potassium’s role and mechanism of action in enabling the hyperosmotic tolerance of P. protegens. Potassium was observed to significantly improve the growth of P. protegens under hyperosmotic conditions. Four functionally redundant potassium transporters, KdpA1, KdpA2, TrkH, and Kup, were identified in P. protegens, of which KdpA2 and TrkH were particularly important for its growth under hyperosmotic conditions. Potassium enhanced the biofilm formation and cell membrane stability of P. protegens under hyperosmotic conditions. In addition, we revealed that K+ stimulates the expression of several genes related to DNA damage repair in P. protegens under hyperosmotic conditions. Further experiments revealed that the DNA repair-related recG induced by potassium contributes to P. protegens’ hyperosmotic tolerance. We also found that the sigma factor RpoN participates in the hyperosmotic adaptation of P. protegens. Furthermore, we revealed that the opuCABCD operon, whose expression is induced by potassium through RpoN, serves as the key pathway through which betaine, choline, and carnitine improve the hyperosmotic tolerance of P. protegens.

OBJECTIVE:This study aims to comprehensively investigate immune-cell landscapes in ankylosing spondylitis (AS) patients and explore longitudinal immunophenotyping changes induced by biological agents. METHODS:We employed mass cytometry with 35 cellular markers to analyze blood samples from 34 AS patients and 13 healthy controls (HC). Eleven AS patients were re-evaluated 1 month (4 patients) and 3 months (7 patients) after treatment with biological agents. Flow Self-Organizing Maps (FlowSOM) clustering was performed to identify specific cellular metaclusters. We compared cellular abundances across distinct subgroups and validated subset differences using gating strategies in flow cytometry scatter plots, visualized with FlowJo software. The proportions of differential subsets were then used for intercellular and clinical correlation analysis, as well as for constructing diagnostic models based on the random forest algorithm. RESULTS:In AS patients, we identified and validated nine different immune-cell subsets compared to HC. Three subsets increased: helper T-cell 17 (Th17), mucosa-associated invariant T-cell (MAIT), and classical monocytes (CM). Six subsets decreased: effector memory T-cell (TEM), naïve B cells, transitional B cells, IL10+ memory B cells, non-classical monocytes (NCM), and neutrophils. Treatments with biological agents could rectify cellular abnormalities, particularly the imbalance of CM/NCM. Furthermore, these subsets may serve as biomarkers for assessing disease activity and constructing effective diagnostic models for AS. CONCLUSION:These findings provide novel insights into the specific patterns of immune cell in AS, facilitating the further development of novel biomarkers and potential therapeutic targets for AS patients.

Background Primary Sjögren's syndrome (pSS) is an autoimmune condition that causes harm to exocrine glands and also has extra-glandular manifestations (EGM). pSS patients with EGM have a worse prognosis than those with only sicca symptoms. Previous studies have shown that the minor salivary glands (MSG) of pSS patients exhibit a unique profile of cytokines and chemokines compared to healthy controls. However, there is a lack of research comparing pSS with EGM (pSS-EGM) and pSS without EGM (pSS-non-EGM). This study aims to explore potential biomarkers associated with pSS, particularly pSS with EGM. Methods By utilizing RNA sequencing, we conducted an analysis on the gene expression profiles of MSG in 63 patients diagnosed with pSS, as well as 12 non-pSS individuals. Furthermore, we also investigated the MSG of pSS patients, both with and without EGM. Through bioinformatics analysis, we identified genes with differential expression (DEGs) and determined the core hub genes using PPI network. We then analyzed the top 20 DEGs and their correlation with the patients' clinical characteristics, and validated our findings using peripheral blood plasma. Results A total of 725 differentially expressed genes (DEGs) were identified in the comparison between pSS and non-pSS groups, and 727 DEGs were observed between pSS-EGM and pSS-non-EGM. It is noteworthy that the expression levels of CXCL9 were higher in both pSS patients and pSS-EGM when compared to the control group. Taking into consideration the significance of the top 20 DEGs in relation to clinical parameters and the central hub genes, we ultimately chose CXCL9 . In comparison to the non-pSS group, pSS patients exhibited notably greater expression of the CXCL9 gene in the MSG, as well as higher levels of CXCL9 protein in their plasma ( p < 0.001). Furthermore, the expression of the CXCL9 gene and levels of CXCL9 protein were notably higher in pSS patients accompanied by EGM and those with SSA antibodies. Additionally, a correlation was found between the expression of the CXCL9 gene and the EULAR Sjogren’s Syndrome Disease Activity Index (ESSDAI), as well as with immunoglobulin G (IgG) levels and erythrocyte sedimentation rate (ESR). Meanwhile, the protein levels of CXCL9 were found to be correlated with IgG levels and ESSDAI. Conclusion CXCL9 proves to be a valuable biomarker in pSS, specifically due to its strong ability to differentiate between pSS patients with EGM and those without EGM. There is a significant correlation between CXCL9 and various clinical parameters both at the gene and protein level. Therefore, CXCL9 could be a potential target for future treatment of pSS.

ABSTRACT Pseudomonas protegens can serve as an agricultural biocontrol agent. P. protegens often encounters hyperosmotic stress during industrial production and field application. The ability of P. protegens to withstand hyperosmotic stress is important for its application as a biocontrol agent. AlgU is a global regulator responsible for stress response and biocontrol ability. However, the specific regulatory role of AlgU in the hyperosmotic adaptation of P. protegens is poorly understood. In this study, we found that the AlgU mutation disrupted the hyperosmotic tolerance of P. protegens . Many genes and metabolites related to cell envelope formation were significantly downregulated in Δ algU compared with that in the wild-type (WT) strain under hyperosmotic conditions, and we found that the algU mutation caused membrane integrity to be compromised and increased membrane permeability. Further experiments revealed that the cell envelope integrity protein TolA, which is regulated by AlgU, contributes to cell membrane stability and osmotic tolerance in P. protegens . In addition, several genes related to oxidative stress response were significantly downregulated in Δ algU , and higher levels of intracellular reactive oxygen species were found in Δ algU . Furthermore, we found that the synthesis of N-acetyl glutaminyl glutamine amide is directly regulated by AlgU and contributes to the hyperosmotic adaptation of P. protegens . This study revealed the mechanisms of AlgU’s participation in osmotic tolerance in P. protegens , and it provides potential molecular targets for research on the hyperosmotic adaptation of P. protegens . IMPORTANCE In this study, we found that the extracytoplasmic function sigma factor AlgU is essential for the survival of P. protegens under hyperosmotic conditions. We provided evidence supporting the roles of AlgU in influencing cell membrane stability, intracellular reactive oxygen species (ROS) accumulation, and dipeptide N-acetylglutaminylglutamine amide (NAGGN) synthesis in P. protegens under hyperosmotic conditions. Our findings revealed the mechanisms of AlgU’s participation in hyperosmotic stress tolerance in P. protegens, and they provide potential molecular targets for research on the hyperosmotic adaptation of P. protegens , which is of value in improving the biocontrol ability of P. protegens .

ABSTRACT Current microbiome signatures for chronic diseases such as diabetic kidney disease (DKD) are mainly based on low-resolution taxa such as genus or phyla and are often inconsistent among studies. In microbial ecosystems, bacterial functions are strain specific, and taxonomically different bacteria tend to form co-abundance functional groups called guilds. Here, we identified guild-level signatures for DKD by performing in-depth metagenomic sequencing and conducting genome-centric and guild-based analysis on fecal samples from 116 DKD patients and 91 healthy subjects. Redundancy analysis on 1,543 high-quality metagenome-assembled genomes (HQMAGs) identified 54 HQMAGs that were differentially distributed among the young healthy control group, elderly healthy control group, early-stage DKD patients (EDG), and late-stage DKD patients (LDG). Co-abundance network analysis classified the 54 HQMAGs into two guilds. Compared to guild 2, guild 1 contained more short-chain fatty acid biosynthesis genes and fewer genes encoding uremic toxin indole biosynthesis, antibiotic resistance, and virulence factors. Guild indices, derived from the total abundance of guild members and their diversity, delineated DKD patients from healthy subjects and between different severities of DKD. Age-adjusted partial Spearman correlation analysis showed that the guild indices were correlated with DKD disease progression and with risk indicators of poor prognosis. We further validated that the random forest classification model established with the 54 HQMAGs was also applicable for classifying patients with end-stage renal disease and healthy subjects in an independent data set. Therefore, this genome-level, guild-based microbial analysis strategy may identify DKD patients with different severity at an earlier stage to guide clinical interventions. IMPORTANCE Traditionally, microbiome research has been constrained by the reliance on taxonomic classifications that may not reflect the functional dynamics or the ecological interactions within microbial communities. By transcending these limitations with a genome-centric and guild-based analysis, our study sheds light on the intricate and specific interactions between microbial strains and diabetic kidney disease (DKD). We have unveiled two distinct microbial guilds with opposite influences on host health, which may redefine our understanding of microbial contributions to disease progression. The implications of our findings extend beyond mere association, providing potential pathways for intervention and opening new avenues for patient stratification in clinical settings. This work paves the way for a paradigm shift in microbiome research in DKD and potentially other chronic kidney diseases, from a focus on taxonomy to a more nuanced view of microbial ecology and function that is more closely aligned with clinical outcomes.

Objective Primary Sjögren's Syndrome (pSS) is a complex autoimmune disorder characterized by diverse clinical manifestations yet lacking effective therapeutic strategies currently. This study aims to gain a thorough understanding of the clinical landscape of pSS and further delineate its clinical subtypes, thereby enabling the efficient management for pSS. Methods We conducted a cross-sectional observational study of 1318 pSS patients. The pSS patients were categorized and compared based on gender, anti-SSA antibodies, and labial salivary gland biopsies (LGSB). Unsupervised clustering analysis was employed to identify pSS subtypes using systemic involvement among patients. Furthermore, we assessed clinical and biological variances among these subtypes. Results Through group comparisons, we observed more pronounced extraglandular manifestations among male patients, SSA-negative group, and those with positive LGSB results. Based on systemic involvement, pSS patients were categorized into four groups. C1 exhibited minimal systemic involvement, lacking hematologic or serologic manifestations, with the lowest ESSDAI scores. C2 presented with serologic changes in all patients, partial joint involvement, and no hematologic systemic manifestations. C3 lacked joint involvement but all members displayed hematologic systemic involvement, with higher rates of renal, cutaneous, and systemic manifestations. C4 encompassed patients with joint and hematologic involvement, displaying the highest ESSDAI scores. The positivity rates of antibodies, immunological parameters, and inflammatory markers exhibited significant differences among the groups. Furthermore, notable variances were observed in the expression of peripheral blood transcriptomic modules among these groups. Conclusion In this cohort study, we summarized the clinical characteristics of Chinese patients with pSS and identified four distinct subgroups of pSS based on systemic involvement, revealing clinical and molecular disparities that unveil distinct pathobiological endotypes. Our findings hold significant implications for clinical management.

Allogeneic chimeric antigen receptor (CAR)-T cells hold great promise for expanding the accessibility of CAR-T therapy, whereas the risks of allograft rejection have hampered its application. Here, we genetically engineered healthy-donor-derived, CD19-targeting CAR-T cells using CRISPR-Cas9 to address the issue of immune rejection and treated one patient with refractory immune-mediated necrotizing myopathy and two patients with diffuse cutaneous systemic sclerosis with these cells. This study was registered at ClinicalTrials.gov (NCT05859997). The infused cells persisted for over 3 months, achieving complete B cell depletion within 2 weeks of treatment. During the 6-month follow-up, we observed deep remission without cytokine release syndrome or other serious adverse events in all three patients, primarily shown by the significant improvement in the clinical response index scores for the two diseases, respectively, and supported by the observations of reversal of inflammation and fibrosis. Our results demonstrate the high safety and promising immune modulatory effect of the off-the-shelf CAR-T cells in treating severe refractory autoimmune diseases.