bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluating the Impact of Dropout and Genotyping Error on SNP-Based Kinship Analysis With Forensic Samples
Authors: Turner Stephen D. , Nagraj V.P. , Scholz Matthew , Jessa Shakeel , Acevedo Carlos , Ge Jianye , Woerner August E. , Budowle Bruce
Published: June 2022

Technological advances in sequencing and single nucleotide polymorphism (SNP) genotyping microarray technology have facilitated advances in forensic analysis beyond short tandem repeat (STR) profiling, enabling the identification of unknown DNA samples and distant relationships. Forensic genetic genealogy (FGG) has facilitated the identification of distant relatives of both unidentified remains and unknown donors of crime scene DNA, invigorating the use of biological samples to resolve open cases. Forensic samples are often degraded or contain only trace amounts of DNA. In this study, the accuracy of genome-wide relatedness methods and identity by descent (IBD) segment approaches was evaluated in the presence of challenges commonly encountered with forensic data: missing data and genotyping error. Pedigree whole-genome simulations were used to estimate the genotypes of thousands of individuals with known relationships using multiple populations with different biogeographic ancestral origins. Simulations were also performed with varying error rates and types. Using these data, the performance of different methods for quantifying relatedness was benchmarked across these scenarios. When the genotyping error was low (<1%), IBD segment methods outperformed genome-wide relatedness methods for close relationships and are more accurate at distant relationship inference. However, with an increasing genotyping error (1–5%), methods that do not rely on IBD segment detection are more robust and outperform IBD segment methods. The reduced call rate had little impact on either class of methods. These results have implications for the use of dense SNP data in forensic genomics for distant kinship analysis and FGG, especially when the sample quality is low.
Conserved 3′ UTR of Severe Acute Respiratory Syndrome Coronavirus 2: Potential Therapeutic Targets
Authors: Park Jae Hyun , Moon Jisook
Published: June 2022

Our previous paper showed that microRNAs (miRNAs) present within human placental or mesenchymal stem cell-derived extracellular vesicles (EVs) directly interacted with the RNA genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), inhibiting viral replication. In this paper, we analyzed whether these miRNAs could exert antiviral activity against other variants of SARS-CoV-2. We downloaded compete SARS-CoV-2 genome data submitted to the National Center for Biotechnology Information for each SARS-CoV-2 variant, aligned the data to the reference SARS-CoV-2 genome sequence, and then confirmed the presence of 3′ untranslated region (UTR) mutations. We identified one type of 3′ UTR mutation in the Alpha variant, four in the Beta variant, four in the Gamma variant, three in the Delta variant, and none in the Omicron variant. Our findings indicate that 3′ UTR mutations rarely occur as persistent mutations. Interestingly, we further confirmed that this phenomenon could suppress virus replication in the same manner as the previously discovered interaction of placental-EV-derived miRNA with 3′ UTRs of SARS-CoV-2. Because the 3′ UTR of the SARS-CoV-2 RNA genome has almost no mutations, it is expected to be an effective therapeutic target regardless of future variants. Thus, a therapeutic strategy targeting the 3′ UTR of SARS-CoV-2 is likely to be extremely valuable, and such an approach is also expected to be applied to all RNA-based virus therapeutics.
Emerging Roles of T Helper Cells in Non-Infectious Neuroinflammation: Savior or Sinner
Authors: Liu Wenbin , Fan Meiyang , Lu Wen , Zhu Wenhua , Meng Liesu , Lu Shemin
Published: June 2022

CD4+T cells, also known as T helper (Th) cells, contribute to the adaptive immunity both in the periphery and in the central nervous system (CNS). At least seven subsets of Th cells along with their signature cytokines have been identified nowadays. Neuroinflammation denotes the brain’s immune response to inflammatory conditions. In recent years, various CNS disorders have been related to the dysregulation of adaptive immunity, especially the process concerning Th cells and their cytokines. However, as the functions of Th cells are being discovered, it’s also found that their roles in different neuroinflammatory conditions, or even the participation of a specific Th subset in one CNS disorder may differ, and sometimes contrast. Based on those recent and contradictory evidence, the conflicting roles of Th cells in multiple sclerosis, Alzheimer’s disease, Parkinson’s disease, epilepsy, traumatic brain injury as well as some typical mental disorders will be reviewed herein. Research progress, limitations and novel approaches concerning different neuroinflammatory conditions will also be mentioned and compared.
Alt a 1 Promotes Allergic Asthma In Vivo Through TLR4-Alveolar Macrophages
Authors: Hernandez-Ramirez Guadalupe , Pazos-Castro Diego , Gonzalez-Klein Zulema , Resuela-Gonzalez Jose Luis , Fernandez-Bravo Sergio , Palacio-Garcia Lucia , Esteban Vanesa , Garrido-Arandia Maria , Tome-Amat Jaime , Diaz-Perales Araceli
Published: June 2022

The mold Alternaria alternata is one of the main sources of asthma exacerbation, being its major allergen, Alt a 1, indispensable for its development. The main objective of this work was to answer two main questions: 1) can Alt a 1 by itself (without any other context) induce an asthmatic profile in vivo?; and 2) Which molecular mechanisms take place during this phenomenon? To answer both questions, we have developed a mouse model of allergic asthma using only Alt a 1 for mice sensitization. We also made use of in-vitro cellular models and computational studies to support some aspects of our hypothesis. Our results showed that Alt a 1 can induce an asthmatic phenotype, promoting tissue remodeling and infiltration of CD45+ cells, especially eosinophils and macrophages (Siglec F+ and F4/80+). Also, we have found that Alt a 1 sensitization is mediated by the TLR4-macrophage axis.
IL-1α and IL-36 Family Cytokines Can Undergo Processing and Activation by Diverse Allergen-Associated Proteases
Authors: Frezza Valentina , Najda Zaneta , Davidovich Pavel , Sullivan Graeme P. , Martin Seamus J.
Published: June 2022

Inflammation driven by environmental allergens is an important source of morbidity in diseases such as asthma and eczema. How common allergens promote inflammation is still poorly understood, but previous studies have implicated the protease activity associated with many allergens as an important component of the pro-inflammatory properties of these agents. The IL-1 family cytokine, IL-33, has recently been shown to undergo processing and activation by proteases associated with multiple common allergens. However, it remains unclear whether the sensing of exogenous protease activity—as a proxy for the detection of invasive microbes, allergens and parasitic worms—is a general property of IL-1 family cytokines. In common with the majority of IL-1 family members, cytokines within the IL-36 sub-family (IL-36α, IL-36β and IL-36γ) are expressed as inactive precursors that require proteolysis within their N-termini for activation. Here we show that proteases associated with multiple common allergens of plant, insect, fungal and bacterial origin (including: Aspergillus fumigatus, ragweed, rye, house dust mite, cockroach and Bacillus licheniformis) are capable of processing and activating IL-36 family cytokines, with IL-36β being particularly susceptible to activation by multiple allergens. Furthermore, extracts from several allergens also processed and enhanced IL-1α activity. This suggests that multiple IL-1 family cytokines may serve as sentinels for exogenous proteases, coupling detection of such activity to unleashing the pro-inflammatory activity of these cytokines. Taken together with previous data on the diversity of proteases capable of activating IL-1 family cytokines, this suggests that members of this cytokine family may function as ‘activity recognition receptors’ for aberrant protease activity associated with infection, tissue injury or programmed necrosis.
Diagnostic and Predictive Values of Ferroptosis-Related Genes in Child Sepsis
Authors: Li Zhi , Zhang Chi , Liu Yiqi , Wang Fang , Zhao Baoling , Yang Junmei , Zhao Yongjing , Zhao Hong , Wang Guiqiang
Published: June 2022

Background

Early diagnosis of sepsis in children was essential to reducing mortality. This study aimed to explore the value of ferroptosis-related genes in children with sepsis.

Methods

We screened the septic children microarray dataset from the GEO database and analyzed the ferroptosis-related differentially expressed genes (DEGs). A functional analysis of ferroptosis-related DEGs was performed. The protein–protein interaction network was used to identify hub genes. We explored the immune landscape of sepsis and controls. The value of hub genes in diagnosing sepsis was tested in the training (GSE26440) and validation sets (GSE13904), and ELISA was used to verify their diagnostic value in children with sepsis in our hospital.

Results

A total of 2,103 DEGs in GSE26440 were obtained, of which ferroptosis-related DEGs were 34. Enrichment analysis showed significant enrichment in the ferroptosis and hypoxia pathways (i.e., HIF-1 pathway). The top three genes (HMOX1, MAPK14, TLR4) were selected as hub genes. Immunological analysis suggested that 10 cell types (i.e., CD8/CD4 T cells) were lower in sepsis. Immune checkpoint-related genes CD274 (PD-L1), HAVCR2 (TIM3), and SIGLEC15 were overexpressed in sepsis. The AUROC for the diagnosis of sepsis for HMOX1 and TLR4 ranged from 0.77 to 0.81, while the AUROC of MAPK14 reached 0.935 and 0.941 in the training and validation sets. Serum ELISA results of HMOX1 and TLR4 showed no significant difference in differentiating sepsis. The AUROC of MAPK14 was 0.877. When the diagnostic threshold was 74.852 ng/ml, the sensitivity and specificity were 0.906 and 0.719, respectively.

Conclusion

Ferroptosis-related gene MAPK14 is of considerable value in the early diagnosis of sepsis in children.
Antigenic Determinants of SARS-CoV-2-Specific CD4+ T Cell Lines Reveals M Protein-Driven Dysregulation of Interferon Signaling
Authors: Gazzinelli-Guimaraes Pedro H. , Sanku Gayatri , Sette Alessandro , Weiskopf Daniela , Schaughency Paul , Lack Justin , Nutman Thomas B.
Published: June 2022

We generated CD4+ T cell lines (TCLs) reactive to either SARS-CoV-2 spike (S) or membrane (M) proteins from unexposed naïve T cells from six healthy donor volunteers to understand in fine detail whether the S and M structural proteins have intrinsic differences in driving antigen-specific CD4+ T cell responses. Having shown that each of the TCLs were antigen-specific and antigen-reactive, single cell mRNA analyses demonstrated that SARS-CoV-2 S and M proteins drive strikingly distinct molecular signatures. Whereas the S-specific CD4+ T cell transcriptional signature showed a marked upregulation of CCL1, CD44, IL17RB, TNFRSF18 (GITR) and IGLC3 genes, in general their overall transcriptome signature was more similar to CD4+ T cell responses induced by other viral antigens (e.g. CMV). However, the M protein-specific CD4+ TCLs have a transcriptomic signature that indicate a marked suppression of interferon signaling, characterized by a downregulation of the genes encoding ISG15, IFITM1, IFI6, MX1, STAT1, OAS1, IFI35, IFIT3 and IRF7 (a molecular signature which is not dissimilar to that found in severe COVID-19). Our study suggests a potential link between the antigen specificity of the SARS-CoV-2-reactive CD4+ T cells and the development of specific sets of adaptive immune responses. Moreover, the balance between T cells of significantly different specificities may be the key to understand how CD4+ T cell dysregulation can determine the clinical outcomes of COVID-19.
Immunogenicity of SARS-CoV-2 Trimeric Spike Protein Associated to Poly(I:C) Plus Alum
Authors: dos-Santos Júlio Souza , Firmino-Cruz Luan , da Fonseca-Martins Alessandra Marcia , Oliveira-Maciel Diogo , Perez Gustavo Guadagnini , Roncaglia-Pereira Victor A. , Dumard Carlos H. , Guedes-da-Silva Francisca H. , Santos Ana C. Vicente , Leandro Monique dos Santos , Ferreira Jesuino Rafael Machado , Guimarães-Pinto Kamila , Conde Luciana , Rodrigues Danielle A. S. , Silva Marcus Vinicius de Mattos , Alvim Renata G. F. , Lima Tulio M. , Marsili Federico F. , Abreu Daniel P. B. , Ferreira Jr. Orlando C. , Mohana Borges Ronaldo da Silva , Tanuri Amilcar , Souza Thiago Moreno L. , Rossi-Bergmann Bartira , Vale André M. , Silva Jerson Lima , de Oliveira Andréa Cheble , Filardy Alessandra D’Almeida , Gomes Andre M. O. , de Matos Guedes Herbert Leonel
Published: June 2022

The SARS-CoV-2 pandemic has had a social and economic impact worldwide, and vaccination is an efficient strategy for diminishing those damages. New adjuvant formulations are required for the high vaccine demands, especially adjuvant formulations that induce a Th1 phenotype. Herein we assess a vaccination strategy using a combination of Alum and polyinosinic:polycytidylic acid [Poly(I:C)] adjuvants plus the SARS-CoV-2 spike protein in a prefusion trimeric conformation by an intradermal (ID) route. We found high levels of IgG anti-spike antibodies in the serum by enzyme linked immunosorbent assay (ELISA) and high neutralizing titers against SARS-CoV-2in vitroby neutralization assay, after two or three immunizations. By evaluating the production of IgG subtypes, as expected, we found that formulations containing Poly(I:C) induced IgG2a whereas Alum did not. The combination of these two adjuvants induced high levels of both IgG1 and IgG2a. In addition, cellular immune responses of CD4+and CD8+T cells producing interferon-gamma were equivalent, demonstrating that the Alum + Poly(I:C) combination supported a Th1 profile. Based on the high neutralizing titers, we evaluated B cells in the germinal centers, which are specific for receptor-binding domain (RBD) and spike, and observed that more positive B cells were induced upon the Alum + Poly(I:C) combination. Moreover, these B cells produced antibodies against both RBD and non-RBD sites. We also studied the impact of this vaccination preparation [spike protein with Alum + Poly(I:C)] in the lungs of mice challenged with inactivated SARS-CoV-2 virus. We found a production of IgG, but not IgA, and a reduction in neutrophil recruitment in the bronchoalveolar lavage fluid (BALF) of mice, suggesting that our immunization scheme reduced lung inflammation. Altogether, our data suggest that Alum and Poly(I:C) together is a possible adjuvant combination for vaccines against SARS-CoV-2 by the intradermal route.
Altered Balance of Pro-Inflammatory Immune Cells to T Regulatory Cells Differentiates Symptomatic From Asymptomatic Individuals With Anti-Nuclear Antibodies
Authors: Gupta Rashi , Vanlieshout Emma , Manion Kieran , Bonilla Dennisse , Kim Michael , Muñoz-Grajales Carolina , Nassar Carol , Johnson Sindhu R. , Hiraki Linda T. , Ahmad Zareen , Touma Zahi , Bookman Arthur , Wither Joan E.
Published: June 2022

Systemic Autoimmune Rheumatic Diseases (SARDs) are characterized by the production of anti-nuclear antibodies (ANAs). ANAs are also seen in healthy individuals and can be detected years before disease onset in SARD. Both the immunological changes that promote development of clinical symptoms in SARD and those that prevent autoimmunity in asymptomatic ANA+ individuals (ANA+ NS) remain largely unexplored. To address this question, we used flow cytometry to examine peripheral blood immune populations in ANA+ individuals, with and without SARD, including 20 individuals who subsequently demonstrated symptom progression. Several immune populations were expanded in ANA+ individuals with and without SARD, as compared with ANA- healthy controls, particularly follicular and peripheral T helper, and antibody-producing B cell subsets. In ANA+ NS individuals, there were significant increases in T regulatory subsets and TGF-ß1 that normalized in SARD patients, whereas in SARD patients there were increases in Th2 and Th17 helper cell levels as compared with ANA+ NS individuals, resulting in a shift in the balance between inflammatory and regulatory T cell subsets. Patients with SARD also had increases in the proportion of pro-inflammatory innate immune cell populations, such as CD14+ myeloid dendritic cells, and intermediate and non-classical monocytes, as compared to ANA+ NS individuals. When comparing ANA+ individuals without SARD who progressed clinically over the subsequent 2 years with those who did not, we found that progressors had significantly increased T and B cell activation, as well as increased levels of LAG3+ T regulatory cells and TGF-ß1. Collectively, our findings suggest that active immunoregulation prevents clinical autoimmunity in ANA+ NS and that this becomes impaired in patients who progress to SARD, resulting in an imbalance favoring inflammation.
Therapeutic Potential of Photosynthetic Microorganisms for Visceral Leishmaniasis: An Immunological Analysis
Authors: Vaitkevicius-Antão Victor , Moreira-Silva Jady , Reino Isabelle Barreto da Silva Moreira , Melo Maria Gabriella Nunes de , Silva-Júnior José Noé da , Andrade Alexsandra Frazão de , Araújo Paulo Sérgio Ramos de , Bezerra Raquel Pedrosa , Marques Daniela de Araújo Viana , Ferreira Silvana , Pessoa-e-Silva Rômulo , Lorena Virginia Maria Barros de , Paiva-Cavalcanti Milena de
Published: June 2022

New therapeutic strategies for visceral leishmaniasis (VL) have been studied, and the development of an immunotherapeutic agent that modulates the host’s immune response is necessary. The aim of this study was to evaluate in vitro the bioactive extracts of photosynthetic microorganisms (PMs) for their leishmanicidal/leishmanistatic and immunomodulatory potentials. Bioactive extracts from PMs (Arthrospira platensis and Dunaliella tertiolecta) were obtained by sonication. Reference drugs, miltefosine (MTF) and N-methylglucamine antimoniate (SbV), were also evaluated. The selectivity index (SI) of treatments was determined by assays of inhibitory concentration (IC50) in Leishmania infantum cells and cytotoxic concentrations (CC50) in human peripheral blood mononuclear cells by the MTT method. The immune response was evaluated in healthy human cells by the production of cytokines and nitric oxide (NO) and the gene expression of Tbx21, GATA3, RORc, and FOXP3, using four concentrations (CC50, ½ CC50, ¼ CC50, and IC50) for in-vitro stimulation. Based on the data obtained, we observed that the extracts of D. tertiolecta (SI = 4.7) and A. platensis (SI = 3.8) presented better results when compared to SbV (SI = 2.1). When analyzing the immune response results, we identified that the extracts of PMs stimulated the production of cytokines of the Th1 profile more than the reference drugs. The extracts also demonstrated the ability to stimulate NO synthesis. Regarding gene expression, in all concentrations of A. platensis extracts, we found a balance between the Th1/Th2 profile, with the average expression of the Tbx21 gene more than the GATA3 in the highest concentration (CC50). Regarding the extract of D. tertiolecta, we can observe that, in the lowest concentrations, a balance between all the genes was present, with the average expression of the GATA3 gene being lower than the others. The best result was found in the ½ CC50 concentration, stimulating a balanced positive expression between the Th1×Th17×Treg profiles, with a negative expression of GATA3. Thus, PM extracts showed promising results, presenting low toxicity, leishmanicidal/leishmanistatic activity, and induction of the immune response, which could be potential therapeutic candidates for VL.
Integrated Analysis of Gene Co-Expression Network and Prediction Model Indicates Immune-Related Roles of the Identified Biomarkers in Sepsis and Sepsis-Induced Acute Respiratory Distress Syndrome
Authors: Ming Tingqian , Dong Mingyou , Song Xuemin , Li Xingqiao , Kong Qian , Fang Qing , Wang Jie , Wu Xiaojing , Xia Zhongyuan
Published: June 2022

Sepsis is a series of clinical syndromes caused by immunological response to severe infection. As the most important and common complication of sepsis, acute respiratory distress syndrome (ARDS) is associated with poor outcomes and high medical expenses. However, well-described studies of analysis-based researches, especially related bioinformatics analysis on revealing specific targets and underlying molecular mechanisms of sepsis and sepsis-induced ARDS (sepsis/se-ARDS), still remain limited and delayed despite the era of data-driven medicine. In this report, weight gene co-expression network based on data from a public database was constructed to identify the key modules and screen the hub genes. Functional annotation by enrichment analysis of the modular genes also demonstrated the key biological processes and signaling pathway; among which, extensive immune-involved enrichment was remarkably associated with sepsis/se-ARDS. Based on the differential expression analysis, least absolute shrink and selection operator, and multivariable logistic regression analysis of the screened hub genes, SIGLEC9, TSPO, CKS1B and PTTG3P were identified as the candidate biomarkers for the further analysis. Accordingly, a four-gene-based model for diagnostic prediction assessment was established and then developed by sepsis/se-ARDS risk nomogram, whose efficiency was verified by calibration curves and decision curve analyses. In addition, various machine learning algorithms were also applied to develop extra models based on the four genes. Receiver operating characteristic curve analysis proved the great diagnostic and predictive performance of these models, and the multivariable logistic regression of the model was still found to be the best as further verified again by the internal test, training, and external validation cohorts. During the development of sepsis/se-ARDS, the expressions of the identified biomarkers including SIGLEC9, TSPO, CKS1B and PTTG3P were all regulated remarkably and generally exhibited notable correlations with the stages of sepsis/se-ARDS. Moreover, the expression levels of these four genes were substantially correlated during sepsis/se-ARDS. Analysis of immune infiltration showed that multiple immune cells, neutrophils and monocytes in particular, might be closely involved in the process of sepsis/se-ARDS. Besides, SIGLEC9, TSPO, CKS1B and PTTG3P were considerably correlated with the infiltration of various immune cells including neutrophils and monocytes during sepsis/se-ARDS. The discovery of relevant gene co-expression network and immune signatures might provide novel insights into the pathophysiology of sepsis/se-ARDS.
Nanomaterial-Based Zinc Ion Interference Therapy to Combat Bacterial Infections
Authors: Wei Yongbin , Wang Jiaming , Wu Sixuan , Zhou Ruixue , Zhang Kaixiang , Zhang Zhenzhong , Liu Junjie , Qin Shangshang , Shi Jinjin
Published: June 2022

Pathogenic bacterial infections are the second highest cause of death worldwide and bring severe challenges to public healthcare. Antibiotic resistance makes it urgent to explore new antibacterial therapy. As an essential metal element in both humans and bacteria, zinc ions have various physiological and biochemical functions. They can stabilize the folded conformation of metalloproteins and participate in critical biochemical reactions, including DNA replication, transcription, translation, and signal transduction. Therefore, zinc deficiency would impair bacterial activity and inhibit the growth of bacteria. Interestingly, excess zinc ions also could cause oxidative stress to damage DNA, proteins, and lipids by inhibiting the function of respiratory enzymes to promote the formation of free radicals. Such dual characteristics endow zinc ions with unparalleled advantages in the direction of antibacterial therapy. Based on the fascinating features of zinc ions, nanomaterial-based zinc ion interference therapy emerges relying on the outstanding benefits of nanomaterials. Zinc ion interference therapy is divided into two classes: zinc overloading and zinc deprivation. In this review, we summarized the recent innovative zinc ion interference strategy for the treatment of bacterial infections and focused on analyzing the antibacterial mechanism of zinc overloading and zinc deprivation. Finally, we discuss the current limitations of zinc ion interference antibacterial therapy and put forward problems of clinical translation for zinc ion interference antibacterial therapy.
Single-Cell RNA Sequencing Unravels Upregulation of Immune Cell Crosstalk in Relapsed Pediatric Ependymoma
Authors: Wu Haoda , Fu Ruiqing , Zhang Yu-Hong , Liu Zhiming , Chen Zhen-Hua , Xu Jingkai , Tian Yongji , Jin Wenfei , Wong Samuel Zheng Hao , Wu Qing-Feng
Published: June 2022

Ependymoma (EPN) is a malignant glial tumor occurring throughout central nervous system, which commonly presents in children. Although recent studies have characterized EPN samples at both the bulk and single-cell level, intratumoral heterogeneity across subclones remains a confounding factor that impedes understanding of EPN biology. In this study, we generated a high-resolution single-cell dataset of pediatric ependymoma with a particular focus on the comparison of subclone differences within tumors and showed upregulation of cilium-associated genes in more highly differentiated subclone populations. As a proxy to traditional pseudotime analysis, we applied a novel trajectory scoring method to reveal cellular compositions associated with poor survival outcomes across primary and relapsed patients. Furthermore, we identified putative cell–cell communication features between relapsed and primary samples and showed upregulation of pathways associated with immune cell crosstalk. Our results revealed both inter- and intratumoral heterogeneity in EPN and provided a framework for studying transcriptomic signatures of individual subclones at single-cell resolution.
Added Value of Reanalysis of Whole Exome- and Whole Genome Sequencing Data From Patients Suspected of Primary Immune Deficiency Using an Extended Gene Panel and Structural Variation Calling
Authors: Mørup Sara Bohnstedt , Nazaryan-Petersen Lusine , Gabrielaite Migle , Reekie Joanne , Marquart Hanne V. , Hartling Hans Jakob , Marvig Rasmus L. , Katzenstein Terese L. , Masmas Tania N. , Lundgren Jens , Murray Daniel D. , Helleberg Marie , Borgwardt Line
Published: June 2022

Background

Knowledge of the genetic variation underlying Primary Immune Deficiency (PID) is increasing. Reanalysis of genome-wide sequencing data from undiagnosed patients with suspected PID may improve the diagnostic rate.

Methods

We included patients monitored at the Department of Infectious Diseases or the Child and Adolescent Department, Rigshospitalet, Denmark, for a suspected PID, who had been analysed previously using a targeted PID gene panel (457 PID-related genes) on whole exome- (WES) or whole genome sequencing (WGS) data. A literature review was performed to extend the PID gene panel used for reanalysis of single nucleotide variation (SNV) and small indels. Structural variant (SV) calling was added on WGS data.

Results

Genetic data from 94 patients (86 adults) including 36 WES and 58 WGS was reanalysed a median of 23 months after the initial analysis. The extended gene panel included 208 additional PID-related genes. Genetic reanalysis led to a small increase in the proportion of patients with new suspicious PID related variants of uncertain significance (VUS). The proportion of patients with a causal genetic diagnosis was constant. In total, five patients (5%, including three WES and two WGS) had a new suspicious PID VUS identified due to reanalysis. Among these, two patients had a variant added due to the expansion of the PID gene panel, and three patients had a variant reclassified to a VUS in a gene included in the initial PID gene panel. The total proportion of patients with PID related VUS, likely pathogenic, and pathogenic variants increased from 43 (46%) to 47 (50%), as one patient had a VUS detected in both initial- and reanalysis. In addition, we detected new suspicious SNVs and SVs of uncertain significance in PID candidate genes with unknown inheritance and/or as heterozygous variants in genes with autosomal recessive inheritance in 8 patients.

Conclusion

These data indicate a possible diagnostic gain of reassessing WES/WGS data from patients with suspected PID. Reasons for the possible gain included improved knowledge of genotype-phenotype correlation, expanding the gene panel, and adding SV analyses. Future studies of genotype-phenotype correlations may provide additional knowledge on the impact of the new suspicious VUSs.
Combining Clinical Parameters and Acute Tubular Injury Grading Is Superior in Predicting the Prognosis of Deceased-Donor Kidney Transplantation: A 7-Year Observational Study
Authors: Wang Jiali , Liu Jinqi , Wu Wenrui , Yang Shicong , Liu Longshan , Fu Qian , Li Jun , Chen Xutao , Deng Ronghai , Wu Chenglin , Long Sizhe , Zhang Wujun , Zhang Huanxi , Mao Haiping , Chen Wenfang
Published: June 2022

Background

We developed a pragmatic dichotomous grading criterion to stratify the acute tubular injury (ATI) of deceased-donor kidneys. We intended to verify the predictive value of this criterion for the prognosis of deceased-donor kidney transplantation.

Methods

The allografts with ATI were classified into severe and mild groups. Severe ATI was defined as the presence of extreme and diffuse flattening of the tubular epithelial cells, or denudement of the tubular basement membrane. The clinical delayed graft function (DGF) risk index was calculated based on a regression model for posttransplant DGF using 17 clinical parameters related to donor–recipient characteristics.

Results

A total of 140 recipients were enrolled: 18 severe and 122 mild ATI. Compared with the mild ATI group, the severe ATI group had more donors after cardiac death, higher median donor terminal serum creatinine level (dScr), and longer median cold ischemia time. Severe ATI had a higher DGF rate (55.6% vs 14.6%, p < 0.001), longer DGF recovery time (49.6 vs 26.3 days, p < 0.001), and a lower estimated glomerular filtration rate (eGFR) at 1 month (23.5 vs 54.0 ml/min/1.73 m2, p < 0.001), 3 months (40.4 vs 59.0, p = 0.001), and 6 months after transplant (46.8 vs 60.3, p = 0.033). However, there was no significant difference in eGFR at 1 year or beyond, graft, and patient survival. The predictive value of combined dScr with ATI severity for DGF rate and DGF recovery time was superior to that of dScr alone. The predictive value of the combined DGF risk index with ATI severity for DGF was also better than that of the DGF risk index alone; however, the association of the DGF risk index with DGF recovery time was not identified. Chronic lesions including glomerulosclerosis, interstitial fibrosis, arterial intimal fibrosis, and arteriolar hyalinosis were associated with declined posttransplant 1-year eGFR.

Conclusion

Based on our pragmatic dichotomous grading criterion for ATI in a preimplantation biopsy, donor kidneys with severe ATI increased DGF risk, prolonged DGF recovery, and decreased short-term graft function but demonstrated favorable long-term graft function. Our grading method can offer additive valuable information for assessing donor kidneys with acute kidney injury and may act as an effective supplementary index of the Banff criteria.
TREGking From Gut to Brain: The Control of Regulatory T Cells Along the Gut-Brain Axis
Authors: Choi Juli , Kim Bo-Ram , Akuzum Begum , Chang Leechung , Lee June-Yong , Kwon Ho-Keun
Published: June 2022

The human gastrointestinal tract has an enormous and diverse microbial community, termed microbiota, that is necessary for the development of the immune system and tissue homeostasis. In contrast, microbial dysbiosis is associated with various inflammatory and autoimmune diseases as well as neurological disorders in humans by affecting not only the immune system in the gastrointestinal tract but also other distal organs. FOXP3+ regulatory T cells (Tregs) are a subset of CD4+ helper T cell lineages that function as a gatekeeper for immune activation and are essential for peripheral autoimmunity prevention. Tregs are crucial to the maintenance of immunological homeostasis and tolerance at barrier regions. Tregs reside in both lymphoid and non-lymphoid tissues, and tissue-resident Tregs have unique tissue-specific phenotype and distinct function. The gut microbiota has an impact on Tregs development, accumulation, and function in periphery. Tregs, in turn, modulate antigen-specific responses aimed towards gut microbes, which supports the host–microbiota symbiotic interaction in the gut. Recent studies have indicated that Tregs interact with a variety of resident cells in central nervous system (CNS) to limit the progression of neurological illnesses such as ischemic stroke, Alzheimer’s disease, and Parkinson’s disease. The gastrointestinal tract and CNS are functionally connected, and current findings provide insights that Tregs function along the gut-brain axis by interacting with immune, epithelial, and neuronal cells. The purpose of this study is to explain our current knowledge of the biological role of tissue-resident Tregs, as well as the interaction along the gut-brain axis.
Gut Commensal Parabacteroides goldsteinii MTS01 Alters Gut Microbiota Composition and Reduces Cholesterol to Mitigate Helicobacter pylori-Induced Pathogenesis
Authors: Lai Chih-Ho , Lin Tzu-Lung , Huang Mei-Zi , Li Shiao-Wen , Wu Hui-Yu , Chiu Ya-Fang , Yang Chia-Yu , Chiu Cheng-Hsun , Lai Hsin-Chih
Published: June 2022

Helicobacter pylori infection is closely associated with various gastrointestinal diseases and poses a serious threat to human health owing to its increasing antimicrobial resistance. H. pylori possesses two major virulence factors, vacuolating cytotoxin A (VacA) and cytotoxin-associated gene A (CagA), which are involved in its pathogenesis. Probiotics have recently been used to eradicate H. pylori infection and reduce the adverse effects of antibiotic-based therapies. Parabacteroides goldsteinii MTS01 is a novel next-generation probiotic (NGP) with activities that can alleviate specific diseases by altering the gut microbiota. However, the mechanism by which P. goldsteinii MTS01 exerts its probiotic effects against H. pylori infection remains unclear. Our results showed that administration of P. goldsteinii MTS01 to H. pylori-infected model mice altered the composition of the gut microbiota and significantly reduced serum cholesterol levels, which mitigated H. pylori-induced gastric inflammation. In addition, the pathogenic effects of H. pylori VacA and CagA on gastric epithelial cells were markedly abrogated by treatment with P. goldsteinii MTS01. These results indicate that P. goldsteinii MTS01 can modulate gut microbiota composition and has anti-virulence factor functions, and thus could be developed as a novel functional probiotic for reducing H. pylori-induced pathogenesis.
T Cell-Intrinsic Vitamin A Metabolism and Its Signaling Are Targets for Memory T Cell-Based Cancer Immunotherapy
Authors: Fujiki Fumihiro , Morimoto Soyoko , Katsuhara Akiko , Okuda Akane , Ogawa Saeka , Ueda Eriko , Miyazaki Maki , Isotani Ayako , Ikawa Masahito , Nishida Sumiyuki , Nakajima Hiroko , Tsuboi Akihiro , Oka Yoshihiro , Nakata Jun , Hosen Naoki , Kumanogoh Atsushi , Oji Yusuke , Sugiyama Haruo
Published: June 2022

Memory T cells play an essential role in infectious and tumor immunity. Vitamin A metabolites such as retinoic acid are immune modulators, but the role of vitamin A metabolism in memory T-cell differentiation is unclear. In this study, we identified retinol dehydrogenase 10 (Rdh10), which metabolizes vitamin A to retinal (RAL), as a key molecule for regulating T cell differentiation. T cell-specific Rdh10 deficiency enhanced memory T-cell formation through blocking RAL production in infection model. Epigenetic profiling revealed that retinoic acid receptor (RAR) signaling activated by vitamin A metabolites induced comprehensive epigenetic repression of memory T cell-associated genes, including TCF7, thereby promoting effector T-cell differentiation. Importantly, memory T cells generated by Rdh deficiency and blocking RAR signaling elicited potent anti-tumor responses in adoptive T-cell transfer setting. Thus, T cell differentiation is regulated by vitamin A metabolism and its signaling, which should be novel targets for memory T cell-based cancer immunotherapy.
Multifaceted Roles of the E3 Ubiquitin Ligase RING Finger Protein 115 in Immunity and Diseases
Authors: Wang Mei-Xia , Liuyu Tianzi , Zhang Zhi-dong
Published: June 2022

Ubiquitination is a post-translational modification that plays essential roles in various physiological and pathological processes. Protein ubiquitination depends on E3 ubiquitin ligases that catalyze the conjugation of ubiquitin molecules on lysine residues of targeted substrates. RING finger protein 115 (RNF115), also known as breast cancer associated gene 2 (BCA2) and Rab7-interacting RING finger protein (Rabring7), has been identified as a highly expressed protein in breast cancer cells and tissues. Later, it has been demonstrated that RNF115 catalyzes ubiquitination of a series of proteins to modulate a number of signaling pathways, and thereby regulates viral infections, autoimmunity, cell proliferation and death and tumorigenesis. In this review, we introduce the identification, expression and activity regulation of RNF115, summarize the substrates and functions of RNF115 in different pathways, and discuss the roles of RNF115 as a biomarker or therapeutic target in diseases.
A Generalized Two–Scale Approximation for Ocean Wave Models
Authors: Perrie William , Toulany Bechara , Casey Michael
Published: June 2022

The two-scale approximation (hereafter, TSA) was previously presented as a new method to approximate and estimate transfer rates in wind – wave spectra. It was shown to perform well for a variety of idealized and observed sea state conditions and to compare well with respect to the total Boltzmann integral for nonlinear quadruplet wave-wave interactions. Here, we present a generalized formulation of TSA, allowing for multiple peaked spectra, sheared spectra, sea – swell combinations, etc. This formulation is implemented in a modern operational wave model, WAVEWATCHIII™, and shown to provide a significant improvement over the standard approximation used in wave models, the discrete interaction approximation (DIA). Additional tests involve the simulation of waves generated in Hurricane Teddy (2020).
Trophic Structure and Diet of Predatory Teleost Fishes in a Tropical Demersal Shelf Ecosystem
Authors: Speed Conrad W. , Meekan Mark G. , Birt Matthew J. , Parsons Miles J. G. , McLean Dianne , Taylor Brett M. , Thomas Luke , McCauley Robert , Semmens Jayson M. , Newman Stephen J.
Published: June 2022

Predatory fishes are a major component of many tropical fisheries, although little is known about their diet and trophic structure, which can hinder effective management. We used stable isotopes δ15N and δ13C in conjunction with dietary prey items of five fishes (Lutjanus sebae, Lethrinus punctulatus, Epinephelus areolatus, Epinephelus multinotatus, and Plectropomus maculatus) to describe the diet and trophic structure across this assemblage. A total of 153 isotope and 87 stomach content samples were collected at two locations that were ≈30 km apart, over two sampling trips, separated by three months. There was clear separation of species’ mean δ15N and δ13C values in isotopic space; the highest mean δ15N was exhibited by E. multinotatus (13.50 ± 0.11 SE) and the lowest was L. punctulatus (11.05 ± 0.13). These two species had the lowest overlap of isotopic niche space, whereas the highest overlap occurred between L. sebae and P. maculatus. δ15N increased with fish body size for all species. However, body size was not significantly related to δ13C values for any species. There was a notable shift in both δ15N and δ13C between sampling trips, with δ13C being more depleted in the second trip. There was also a difference in δ13C between locations for all species, suggesting localised foraging. A multiple tissue comparison for L. sebae indicated positive relationships for both δ15N and δ13C between dorsal fin and muscle tissue. Mean δ15N values were the same for both fin (12.1 ± 0.10 SE) and muscle tissue (12.1 ± 0.09 SE), although δ13C was more enriched in fin (-15.6 ± 0.14 SE) compared to muscle tissue (-17.3 ± 0.11 SE). The most common dietary items across species were teleosts and crustaceans, which was consistent with isotope data indicating a reliance on a demersal food web (δ13C values ranging from -18 to -15‰). The results from our study indicate a dynamic spatio-temporal trophic structure and diet for commercially important demersal species and highlight the benefits of a multi-facetted sampling approach.
Gut Microbiota in Systemic Lupus Erythematosus and Correlation With Diet and Clinical Manifestations
Authors: Wang Xiao , Shu Qiang , Song Lijun , Liu Qi , Qu Xiaoxia , Li Ming
Published: June 2022

Despite the existing studies relating systemic lupus erythematosus (SLE) to changes in gut microbiota, the latter is affected by external factors such as diet and living environment. Herein, we compared the diversity and composition of gut microbiota in SLE patients and in their healthy family members who share the same household, to link gut microbiota, diet and SLE clinical manifestations. The study cohort included 19 patients with SLE and 19 of their healthy family members. Daily nutrition was assessed using a food frequency questionnaire (FFQ). Microbiota was analyzed using amplicons from the V4 regions of the 16S rRNA gene, to obtain microbiota diversity, taxa relative abundances and network analysis. The gut microbiota in the SLE group had lower alpha diversity and higher heterogeneity than the control group. SLE patients had decreased Acidobacteria, Gemmatimonadetes, Nitrospirae and Planctomycetes at the phylum level, and increased Streptococcus, Veillonella, Clostridium_XI, and Rothia at the genus level. Streptococcus was extremely enriched among patients with lupus nephritis. Lactobacillus, Clostridium_XlVa, Lachnospiracea_incertae_sedis and Parasutterella OTUs were associated with diet and clinical features of SLE. Finally, the gut microbiota of SLE patients remained different from that in healthy controls even after accounting for living conditions and diet.
Exploring the Impact of Pre-course High-Fidelity Simulation on Professional Socialization of Medical Students in Emergency Medicine Internship Rotation—A Qualitative Approach
Authors: Chang Yu-Che , Nkambule Nothando Sithulile , Chen Shou-Yen , Hsieh Ming-Ju , Chaou Chung-Hsien
Published: June 2022

Background

Medical students in block clerkships constantly adapt to new environments and learn to interact with new people as they rotate between specialties. This frequent change potentially limited interns' opportunities for participation in real clinical practice. The aims of this study were to explore interns' conceptualization of their learning opportunities and experiences in the workplace during an emergency medicine (EM) block internship. In addition, the study also explored how participating in the pre-rotation high-fidelity simulation (HFS) orientation influenced interns' perception of their transition, participation and learning experiences in the real EM setting.

Methods

We implemented a newly developed pre-EM rotation orientation curriculum for interns. This orientation took place on the first day of the 2-week EM internship rotation. Two focus group discussions were held after each simulation training, one immediately after simulation to understand the students' perception and the educational impact of this activity, the other at the end of EM rotation to explore and compare their roles and perception in both simulation activity and the real clinical practice. A total of 151 seventh-year medical students enrolled in the pre-course HFS and post-hoc focus group discussions between 2017 and 2019. We applied thematic analysis to systemically identify, examine, and construct themes.

Results

Four major themes were constructed from the data; 1. Challenges in finding authentic learning experiences within the context of emergency medicine; 2. Effectiveness of the pre-course HFS 3. Limitations of EM internship rotation curriculum and pre-course simulation. 4. Suggestions for EM block-internship curriculum reforms. Our study's key findings indicate that pre-rotation orientation HFS activity, which offered a psychologically safe space for students to explore facets of EM and gain a contextualized understanding of the emergency work culture and environment, was essential for enhancing students' ability to identify and maximize practice affordances in real workplace.

Conclusion

Simulation, facilitates interns' negotiation of legitimate peripheral participation opportunities as they transition into the EM community of practice during their block internship rotation; putting students at the center of the learning process.
Humans and Hoofed Livestock Are the Main Sources of Fecal Contamination of Rivers Used for Crop Irrigation: A Microbial Source Tracking Approach
Authors: Díaz-Gavidia Constanza , Barría Carla , Weller Daniel L. , Salgado-Caxito Marilia , Estrada Erika M. , Araya Aníbal , Vera Leonardo , Smith Woutrina , Kim Minji , Moreno-Switt Andrea I. , Olivares-Pacheco Jorge , Adell Aiko D.
Published: June 2022

Freshwater bodies receive waste, feces, and fecal microorganisms from agricultural, urban, and natural activities. In this study, the probable sources of fecal contamination were determined. Also, antibiotic resistant bacteria (ARB) were detected in the two main rivers of central Chile. Surface water samples were collected from 12 sampling sites in the Maipo (n = 8) and Maule Rivers (n = 4) every 3 months, from August 2017 until April 2019. To determine the fecal contamination level, fecal coliforms were quantified using the most probable number (MPN) method and the source of fecal contamination was determined by Microbial Source Tracking (MST) using the Cryptosporidium and Giardia genotyping method. Separately, to determine if antimicrobial resistance bacteria (AMB) were present in the rivers, Escherichia coli and environmental bacteria were isolated, and the antibiotic susceptibility profile was determined. Fecal coliform levels in the Maule and Maipo Rivers ranged between 1 and 130 MPN/100-ml, and 2 and 30,000 MPN/100-ml, respectively. Based on the MST results using Cryptosporidium and Giardia host-specific species, human, cattle, birds, and/or dogs hosts were the probable sources of fecal contamination in both rivers, with human and cattle host-specific species being more frequently detected. Conditional tree analysis indicated that coliform levels were significantly associated with the river system (Maipo versus Maule), land use, and season. Fecal coliform levels were significantly (p < 0.006) higher at urban and agricultural sites than at sites immediately downstream of treatment centers, livestock areas, or natural areas. Three out of eight (37.5%) E. coli isolates presented a multidrug-resistance (MDR) phenotype. Similarly, 6.6% (117/1768) and 5.1% (44/863) of environmental isolates, in Maipo and Maule River showed and MDR phenotype. Efforts to reduce fecal discharge into these rivers should thus focus on agriculture and urban land uses as these areas were contributing the most and more frequently to fecal contamination into the rivers, while human and cattle fecal discharges were identified as the most likely source of this fecal contamination by the MST approach. This information can be used to design better mitigation strategies, thereby reducing the burden of waterborne diseases and AMR in Central Chile.