bluuebunny/crossref_metadata_2025_split huggingface dataset:
G protein-coupled receptor 183 mediates the sensitization of Burkitt lymphoma tumors to CD47 immune checkpoint blockade by anti-CD20/PI3Kδi dual therapy
Authors: Ribeiro Marcelo Lima , Profitós-Pelejà Núria , Santos Juliana Carvalho , Blecua Pedro , Reyes-Garau Diana , Armengol Marc , Fernández-Serrano Miranda , Miskin Hari P. , Bosch Francesc , Esteller Manel , Normant Emmanuel , Roué Gael 
Published: April 2023

BackgroundImmunotherapy-based regimens have considerably improved the survival rate of B-cell non-Hodgkin lymphoma (B-NHL) patients in the last decades; however, most disease subtypes remain almost incurable. TG-1801, a bispecific antibody that targets CD47 selectively on CD19+ B-cells, is under clinical evaluation in relapsed/refractory (R/R) B-NHL patients either as a single-agent or in combination with ublituximab, a new generation CD20 antibody.MethodsA set of eight B-NHL cell lines and primary samples were cultured in vitro in the presence of bone marrow-derived stromal cells, M2-polarized primary macrophages, and primary circulating PBMCs as a source of effector cells. Cell response to TG-1801 alone or combined with the U2 regimen associating ublituximab to the PI3Kδ inhibitor umbralisib, was analyzed by proliferation assay, western blot, transcriptomic analysis (qPCR array and RNA sequencing followed by gene set enrichment analysis) and/or quantification of antibody-dependent cell death (ADCC) and antibody-dependent cell phagocytosis (ADCP). CRISPR-Cas9 gene edition was used to selectively abrogate GPR183 gene expression in B-NHL cells. In vivo, drug efficacy was determined in immunodeficient (NSG mice) or immune-competent (chicken embryo chorioallantoic membrane (CAM)) B-NHL xenograft models.ResultsUsing a panel of B-NHL co-cultures, we show that TG-1801, by disrupting the CD47-SIRPα axis, potentiates anti-CD20-mediated ADCC and ADCP. This led to a remarkable and durable antitumor effect of the triplet therapy composed by TG-1801 and U2 regimen, in vitro, as well as in mice and CAM xenograft models of B-NHL. Transcriptomic analysis also uncovered the upregulation of the G protein-coupled and inflammatory receptor, GPR183, as a crucial event associated with the efficacy of the triplet combination. Genetic depletion and pharmacological inhibition of GPR183 impaired ADCP initiation, cytoskeleton remodeling and cell migration in 2D and 3D spheroid B-NHL co-cultures, and disrupted macrophage-mediated control of tumor growth in B-NHL CAM xenografts.ConclusionsAltogether, our results support a crucial role for GPR183 in the recognition and elimination of malignant B cells upon concomitant targeting of CD20, CD47 and PI3Kδ, and warrant further clinical evaluation of this triplet regimen in B-NHL.
Clinical analysis of 173 pediatric patients with antibody-mediated autoimmune diseases of the central nervous system: a single-center cohort study
Authors: Kang Qingyun , Liao Hongmei , Yang Liming , Fang Hongjun , Ning Zeshu , Liao Caishi , Gan Siyi , Wu Liwen 
Published: April 2023

BackgroundAntibody-mediated disorders of the central nervous system (CNS) have seen a gradual rise in their incidence and prevalence. This retrospective observational study aimed to investigate the clinical characteristics and short-term prognosis of children with antibody-mediated CNS autoimmune diseases at Hunan Children’s Hospital.MethodsWe collected the clinical data of 173 pediatric patients diagnosed with antibody-mediated CNS autoimmune diseases between June 2014 and June 2021 and analyzed their demographics, clinical features, imaging and laboratory data, treatment, and prognosis.ResultsA total of 187 patients tested positive for anti-neural antibodies and 173 patients were finally diagnosed with antibody-mediated CNS autoimmune diseases after excluding the 14 false-positive cases through clinical phenotypic evaluation and follow-up of treatment outcomes. Of the 173 confirmed patients, 97 (56.06%) were positive for anti-NMDA-receptor antibody, 48 (27.75%) for anti-MOG antibody, 30 (17.34%) for anti-GFAP antibody, 5 (2.89%) for anti-CASPR2 antibody, 3 (1.73%) for anti-AQP4 antibody, 2 (1.16%) for anti-GABABR antibody, and 1 (0.58%) for anti-LGI1antibody. Anti-NMDAR encephalitis was the most commonly seen among the patients, followed by MOG antibody-associated disorders and autoimmune GFAP astrocytopathy. Psycho-behavioral abnormalities, seizures, involuntary movements, and speech disorder were the most common clinical presentations of anti-NMDAR encephalitis, while fever, headache, and disturbance of consciousness or vision were the most seen among patients with MOG antibody-associated disorders or autoimmune GFAP astrocytopathy. The coexistence of multiple anti-neural antibodies was detected in 13 patients, among which 6 cases had coexistent anti-NMDAR and anti-MOG antibodies (including 1 case with anti-GFAP antibody also), 3 cases had coexistent anti-NMDAR and anti-GFAP antibodies, 3 cases had coexistent anti-MOG and anti-GFAP antibodies, 1 case had coexistent anti-NMDAR and anti-CASPR2 antibodies, and 1 case had coexistent anti-GABABR and anti-CASPR2 antibodies. All the survivors were followed up for at least 12 months; 137 recovered completely, 33 had varying sequelae, and 3 died; 22 had one or more relapses.ConclusionAntibody-mediated CNS autoimmune diseases occur in children of all ages. Most such pediatric patients have a good response to immunotherapy. Despite the low mortality rate, some survivors have a non-negligible risk of developing relapses.
Potential common molecular mechanisms between Sjögren syndrome and inclusion body myositis: a bioinformatic analysis and in vivo validation
Authors: Zeng Li , Chen Kai , Xiao Feng , Zhu Chun-yan , Bai Jia-ying , Tan Song , Long Li , Wang Yi , Zhou Qiao 
Published: April 2023

BackgroundInclusion body myositis (IBM) is a slowly progressive inflammatory myopathy that typically affects the quadriceps and finger flexors. Sjögren’s syndrome (SS), an autoimmune disorder characterized by lymphocytic infiltration of exocrine glands has been reported to share common genetic and autoimmune pathways with IBM. However, the exact mechanism underlying their commonality remains unclear. In this study, we investigated the common pathological mechanisms involved in both SS and IBM using a bioinformatic approach.MethodsIBM and SS gene expression profiles were obtained from the Gene Expression Omnibus (GEO). SS and IBM coexpression modules were identified using weighted gene coexpression network analysis (WGCNA), and differentially expressed gene (DEG) analysis was applied to identify their shared DEGs. The hidden biological pathways were revealed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Furthermore, protein−protein interaction (PPI) networks, cluster analyses, and hub shared gene identification were conducted. The expression of hub genes was validated by reverse transcription quantitative polymerase chain reaction (RT−qPCR). We then analyzed immune cell abundance patterns in SS and IBM using single-sample gene set enrichment analysis (ssGSEA) and investigated their association with hub genes. Finally, NetworkAnalyst was used to construct a common transcription factor (TF)-gene network.ResultsUsing WGCNA, we found that 172 intersecting genes were closely related to viral infection and antigen processing/presentation. Based on DEG analysis, 29 shared genes were found to be upregulated and enriched in similar biological pathways. By intersecting the top 20 potential hub genes from the WGCNA and DEG sets, three shared hub genes (PSMB9, CD74, and HLA-F) were derived and validated to be active transcripts, which all exhibited diagnostic values for SS and IBM. Furthermore, ssGSEA showed similar infiltration profiles in IBM and SS, and the hub genes were positively correlated with the abundance of immune cells. Ultimately, two TFs (HDGF and WRNIP1) were identified as possible key TFs.ConclusionOur study identified that IBM shares common immunologic and transcriptional pathways with SS, such as viral infection and antigen processing/presentation. Furthermore, both IBM and SS have almost identical immune infiltration microenvironments, indicating similar immune responses may contribute to their association.
Full characterization of the three pathways of the complement system in patients with systemic lupus erythematosus
Authors: García-González María , Gómez-Bernal Fuensanta , Quevedo-Abeledo Juan C. , Fernández-Cladera Yolanda , González-Rivero Agustín F. , de Vera-González Antonia , de la Rua-Figueroa Iñigo , López-Mejias Raquel , Díaz-González Federico , González-Gay Miguel Á. , Ferraz-Amaro Iván 
Published: April 2023

BackgroundTo date a complete characterization of the components of the complement (C) pathways (CLassical, LEctin and ALternative) in patients with systemic lupus erythematosus (SLE) has not been performed. We aimed to assess the function of these three C cascades through functional assays and the measurement of individual C proteins. We then studied how they relate to clinical characteristics.MethodsNew generation functional assays of the three pathways of the C system were assessed in 284 patients with SLE. Linear regression analysis was performed to study the relationship between the activity, severity, and damage of the disease and C system.ResultsLower values of the functional tests AL and LE were more frequent than those of the CL pathway. Clinical activity was not related to inferior values of C routes functional assays. The presence of increased DNA binding was negatively linked to all three C pathways and products, except for C1-inh and C3a which were positively related. Disease damage revealed a consistent positive, rather than a negative, relationship with pathways and C elements. Anti-ribosomes and anti-nucleosomes were the autoantibodies that showed a greater relationship with C activation, mainly due to the LE and CL pathways. Regarding antiphospholipid antibodies, the most related with C activation were IgG anti-β2GP, predominantly involving the AL pathway.ConclusionNot only the CL route, but also the AL and LE are related to SLE features. C expression patterns are linked to disease profiles. While accrual damage was associated with higher functional tests of C pathways, anti-DNA, anti-ribosomes and anti-nucleosomes antibodies, were the ones that showed a higher relationship with C activation, mainly due to the LE and CL pathways.
Serum amyloid A proteins reduce bone mass during mycobacterial infections
Authors: Gomes Ana Cordeiro , Sousa Daniela Monteiro , Oliveira Tiago Carvalho , Fonseca Óscar , Pinto Ricardo J. , Silvério Diogo , Fernandes Ana Isabel , Moreira Ana C. , Silva Tânia , Teles Maria José , Pereira Luísa , Saraiva Margarida , Lamghari Meriem , Gomes Maria Salomé 
Published: April 2023

IntroductionOsteopenia has been associated to several inflammatory conditions, including mycobacterial infections. How mycobacteria cause bone loss remains elusive, but direct bone infection may not be required.MethodsGenetically engineered mice and morphometric, transcriptomic, and functional analyses were used. Additionally, inflammatory mediators and bone turnover markers were measured in the serum of healthy controls, individuals with latent tuberculosis and patients with active tuberculosis.Results and discussionWe found that infection with Mycobacterium avium impacts bone turnover by decreasing bone formation and increasing bone resorption, in an IFNγ- and TNFα-dependent manner. IFNγ produced during infection enhanced macrophage TNFα secretion, which in turn increased the production of serum amyloid A (SAA) 3. Saa3 expression was upregulated in the bone of both M. avium- and M. tuberculosis-infected mice and SAA1 and 2 proteins (that share a high homology with murine SAA3 protein) were increased in the serum of patients with active tuberculosis. Furthermore, the increased SAA levels seen in active tuberculosis patients correlated with altered serum bone turnover markers. Additionally, human SAA proteins impaired bone matrix deposition and increased osteoclastogenesis in vitro. Overall, we report a novel crosstalk between the cytokine-SAA network operating in macrophages and bone homeostasis. These findings contribute to a better understanding of the mechanisms of bone loss during infection and open the way to pharmacological intervention. Additionally, our data and disclose SAA proteins as potential biomarkers of bone loss during infection by mycobacteria.
A recombinant Modified Vaccinia virus Ankara expressing prME of tick-borne encephalitis virus affords mice full protection against TBEV infection
Authors: Kubinski Mareike , Beicht Jana , Zdora Isabel , Biermann Jeannine , Puff Christina , Gerlach Thomas , Tscherne Alina , Baumgärtner Wolfgang , Osterhaus Albert D. M. E. , Sutter Gerd , Prajeeth Chittappen Kandiyil , Rimmelzwaan Guus F. 
Published: April 2023

IntroductionTick-borne encephalitis virus (TBEV) is an important human pathogen that can cause a serious disease involving the central nervous system (tick-borne encephalitis, TBE). Although approved inactivated vaccines are available, the number of TBE cases is rising, and breakthrough infections in fully vaccinated subjects have been reported in recent years.MethodsIn the present study, we generated and characterized a recombinant Modified Vaccinia virus Ankara (MVA) for the delivery of the pre-membrane (prM) and envelope (E) proteins of TBEV (MVA-prME).ResultsMVA-prME was tested in mice in comparison with a licensed vaccine FSME-IMMUN® and proved to be highly immunogenic and afforded full protection against challenge infection with TBEV.DiscussionOur data indicate that MVA-prME holds promise as an improved next-generation vaccine for the prevention of TBE.
Association between sarcoidosis and HLA polymorphisms in a Czech population from Central Europe: focus on a relationship with clinical outcome and treatment
Authors: Sikorova K. , Osoegawa K. , Kocourkova L. , Strnad A. , Petrkova J. , Fernández-Viña M. A. , Doubkova M. , Petrek M. 
Published: April 2023

BackgroundSarcoidosis is an immune-mediated systemic disease with unknown etiology affecting the lung predominantly. The clinical manifestation of sarcoidosis is rather diverse ranging from Löfgren’s syndrome to fibrotic disease. Also, it differs among patients with distinct geographical and ethnic origins, consistent with environmental and genetic factors’ role in its pathogenesis. Of those, the polymorphic genes of the HLA system have been previously implicated in sarcoidosis. Therefore, we have performed an association study in a well-defined cohort of Czech patients aiming to define how variation in HLA genes, may contribute to disease origin and development.Materials and methodsTotal of the 301 Czech unrelated sarcoidosis patients were diagnosed according to international guidelines. In those, HLA typing was performed using next-generation sequencing. The allele frequencies at six HLA loci (HLA-A,-B,-C,-DRB1,-DQA1, and -DQB1) observed in the patients were compared with HLA allele distribution determined in 309 unrelated healthy Czech subjects; sub-analyses of relationships between HLA and distinct sarcoidosis clinical phenotypes were performed. Associations were assessed by two-tailed Fischer’s exact test with correction for multiple comparisons.ResultsWe report two variants, HLA-DQB1*06:02, and HLA-DQB1*06:04, as risk factors for sarcoidosis, and three variants, HLA-DRB1*01:01, HLA-DQA1*03:01, and HLA-DQB1*03:02 as protective factors. HLA-B*08:01, HLA-C*07:01, HLA-DRB1*03:01, HLA-DQA1*05:01, and HLA-DQB1*02:01 variants associated with Löfgren’s syndrome, a more benign phenotype. HLA- DRB1*03:01 and HLA-DQA1*05:01 alleles were connected with better prognosis—chest X-ray (CXR) stage 1, disease remission, and non-requirement of corticosteroid treatment. The alleles HLA-DRB1*11:01 and HLA-DQA1*05:05 are associated with more advanced disease represented by the CXR stages 2−4. HLA-DQB1*05:03 associated with sarcoidosis extrapulmonary manifestation.ConclusionIn our Czech cohort, we document some associations between sarcoidosis and HLA previously described in other populations. Further, we suggest novel susceptibility factors for sarcoidosis, such as HLA-DQB1*06:04, and characterize associations between HLA and sarcoidosis clinical phenotypes in Czech patients. Our study also extends the role of the 8.1 ancestral haplotype (HLA-A*01:01∼HLA-B*08:01∼HLA-C*07:01∼HLA-DRB1*03:01∼HLA-DQA1*05:01∼HLA-DQB1*02:01), already implicated in autoimmune diseases, as a possible predictor of better prognosis in sarcoidosis. The general translational application of our newly reported findings for personalized patient care should be validated by an independent study from another, international referral center.
Molecular epidemiology and comparative genomics of carbapenemase-producing Escherichia coli isolates from 19 tertiary hospitals in China from 2019 to 2020
Authors: Ko Weihsin , Tseng Songlu , Chou Chiahsin , Li Tianmeng , Li Rose , Zhang Yaqiao , Li Yun , Lv Yuan 
Published: April 2023

BackgroundThe clinical use of carbapenems is facing challenges due to increased carbapenemase-producing Escherichia coli (CP-EC) infections over the past decade. Meanwhile, whole-genome sequencing (WGS) is an important method for bacterial epidemiological research. We aim to provide more gene-based surveys to explore the genomics and occurrence of CP-EC in China.MethodsA total of 780 Escherichia coli isolates were collected by the China Antimicrobial Resistance Surveillance Trial (CARST) from 2019 to 2020. An antibacterial susceptibility test was performed by using the agar dilution method. CP-EC were detected by the modified carbapenem inactivation method (mCIM), EDTA-modified carbapenem inactivation method (eCIM), and polymerase chain reaction (PCR). Homology analysis was performed by multilocus sequence typing (MLST). A conjugation experiment was performed to verify the transferability of plasmids carrying carbapenemase genes. WGS was conducted to explore the gene-environment of the carbapenemase gene.ResultOf the 780 Escherichia coli isolates, 31 isolates were insensitive to carbapenem with a rate of 4%. Among them, 13 CP-EC isolates had transferability of the blaNDM gene. These isolates belonged to nine distinct sequence types (STs), with some correlation. We found that two (2/13, 15.4%) of the CP-EC isolates that were collected from blood specimens were highly pathogenic and also showed high transferability of the blaNDM gene. In addition, eight (8/13, 61.5%) of the CP-EC isolates were found to be multidrug-resistant.ConclusionWith the increasing use of carbapenem, CP-EC isolates accounted for nearly half of the total carbapenem-insensitive Escherichia coli isolates. Our findings highlight the urgent need to pay attention to CP-EC isolates in bloodstream infections and ESBL-producing CP-EC isolates. Based on the One Health concept, we suggest various measures, including the development of bacterial vaccines, antibiotic management, and establishment of better medical environments, to avoid the outbreak of CP-EC.
Changes in soil microbial biomass and organic C pools improve the sustainability of perennial grass and legume system under organic nutrient management
Authors: Rai Arvind Kumar , Basak Nirmalendu , Dixit Anoop Kumar , Rai Suchit Kumar , Das Sanjoy Kumar , Singh J. B. , Kumar Sunil , Kumar T. Kiran , Chandra Priyanka , Sundha Parul , Bedwal Sandeep 
Published: April 2023

IntroductionThe perennial grass–legume cropping system benefits soil because of its high biomass turnover, cover cropping nature, and different foraging behaviors. We investigated the response of soil organic carbon (SOC) pools and their stock to organic and inorganic nutrient management in the Guinea grass and legume (cowpea-Egyptian clover) cropping system.MethodsDepth-wise soil samples were collected after harvesting the Egyptian clover. Based on the ease of oxidation with chromic acid, different pools of SOC oxidizable using the Walkley–Black C method, very labile, labile, less labile, non-labile; and dissolved organic C (DOC), microbial biomass C (MBC), and total organic C (TOC) in soils were analyzed for computing several indices of SOC.Result and discussionAfter 10 years of crop cycles, FYM and NPKF nutrient management recorded greater DOC, MBC, SOC stocks, and C sequestration than the NPK. Stocks of all SOC pools and carbon management index (CMI) decreased with soil depth. A significant improvement in CMI, stratification ratio, sensitivity indices, and sustainable yield index was observed under FYM and NPKF. This grass–legume intercropping system maintained a positive carbon balance sequestered at about 0.8Mg C ha−1 after 10 years without any external input. Approximately 44–51% of the applied carbon through manure was stabilized with SOC under this cropping system. The DOC, MBC, and SOC in passive pools were identified for predicting dry fodder yield. This study concludes that the application of organics in the perennial grass–legume inter cropping system can maintain long-term sustainability, enhance the C sequestration, and offset the carbon footprint of the farm enterprises.
Identification of fungus-growing termite-associated halogenated-PKS maduralactomycin a as a potential inhibitor of MurF protein of multidrug-resistant Acinetobacter baumannii
Authors: Shoaib Muhammad , Shehzadi Iram , Asif Muhammad Umair , Shen Yulong , Ni Jinfeng 
Published: April 2023

Multidrug-resistant Acinetobacter baumannii infections have become a major public health concern globally. Inhibition of its essential MurF protein has been proposed as a potential target for broad-spectrum drugs. This study aimed to evaluate the potential of a novel ecological niche of 374 fungus-growing termite associated Natural Products (NPs). The molecular docking and computational pharmacokinetics screened four compounds, i.e., Termstrin B, Fridamycin A, Maduralactomycin A, and Natalenamide C, as potential compounds that have higher binding affinities and favourable protein-ligand interactions. The compound Maduralactomycin A induced more stability based on its lowest average RMSD value (2.31 Å) and low standard deviation (0.35) supported by the consistent flexibility and β-factor during the protein’s time-dependent motion. While hydrogen bond analysis indicated that Termstrin B has formed the strongest intra-protein interaction, solvent accessibility was in good agreement with Maduralactomycin A compactness. Maduralactomycin A has the strongest binding energy among all the compounds (−348.48 kcal/mol) followed by Termstrin B (−321.19 kcal/mol). Since these findings suggest Maduralactomycin A and Termstrin B as promising candidates for inhibition of MurF protein, the favourable binding energies of Maduralactomycin A make it a more important compound to warrant further investigation. However, experimental validation using animal models and clinical trials is recommended before reaching any final conclusions.