bluuebunny/crossref_metadata_2025 huggingface dataset:
SLC44A2 Frequency, a New TaqMan Real-Time Polymerase Chain Reaction Method for HNA-3A/3B Genotyping, and a New Application of Droplet Digital PCR
Authors: Wang Yufeng , Chen Xihui , Chen Qi , Chen Tangdong , Chen Kun , Wu Yuanming , Wang Li
Published: May 2022

Background: Human neutrophil antigen-3A (HNA-3A) and human neutrophil antigen-3B (HNA-3B) are generated by a single-nucleotide polymorphism (rs2288904, c.461G > A) in exon 7 of the choline transporter-like protein-2 gene (CTL2, also known as SLC44A2). Antibodies to HNA-3 can be generated following blood transfusion or other factors resulting in exposure to HNA-3 antigens. These antibodies can cause transfusion-related acute lung injury (TRALI) or neonatal alloimmune neutropenia (NAIN). This study describes a sensitive and specific TaqMan real-time polymerase chain reaction (PCR) method to screen for the HNA-3 genotype using specific primers and probes designed to detect allelic polymorphisms. Considering the high sensitivity and accuracy of droplet digital PCR (ddPCR) in the identification of the rare SLC44A2*2 allele, we used this technique to identify blood donors with the rare HNA-3B antigen and calculate the allele frequency of SLC44A2 in mixed populations with different proportions.

Methods: DNA samples purified from 208 donors in northwest China were subjected to TaqMan real-time PCR to detect allelic polymorphisms in SLC44A2. The results were confirmed by Sanger sequencing. The rare HNA-3B antigen was detected by ddPCR. SLC44A2 frequency was determined by two-channel ddPCR.

Results: The genotypes of all DNA samples were detected by the TaqMan real-time PCR using specific probes for HNA-3, and the results were consistent with the Sanger sequencing results in respect to the HNA-3A and HNA-3B polymorphisms. The allele frequencies of SLC44A2*1 and SLC44A2*2 in the 208 donors in northwest China were 64.9% (95% confidence interval [CI], 59%–70.8%) and 35.1% (95% CI, 29.2%–41%), respectively. The ratio of SLC44A2*2 alleles was accurately detected in all blood pools by ddPCR but not by TaqMan real-time PCR. This allowed for the SLC44A2 frequency in the population to be accurately inferred.

Conclusion: This new method of detecting SLC44A2 alleles was highly sensitive and specific, as confirmed by Sanger sequencing. ddPCR using the designed probes resulted in successful detection of the rare HNA-3B antigen. Furthermore, we successfully detected the rare HNA-3B antigen and inferred the SLC44A2 frequency by ddPCR using the probes that we designed.
The Mutation Analysis of the AMT Gene in a Chinese Family With Nonketotic Hyperglycinemia
Authors: Zhou Bing-bo , Hui Ling , Zhang Qing-hua , Chen Xue , Zhang Chuan , Zheng Lei , Feng Xuan , Wang Yu-pei , Ding Zhong-jun , Chen Rui-rong , Ma Pan-pan , Liu Fu-rong , Hao Sheng-ju
Published: May 2022

Background: Nonketotic hyperglycinemia is a metabolic disease with autosomal recessive inheritance due to the glycine cleavage system (GCS) defect leading to the accumulation of glycine that causes severe and fatal neurological symptoms in the neonatal period.

Methods: Genomic DNA was extracted from the peripheral blood of the female proband and her family members. The AMT variation was detected in the patient by whole-exome sequencing (WES), and the variant was validated by Sanger sequencing.

Results: The WES showed that there were novel compound heterozygous frameshift variations c.977delA (p.Glu326Glyfs*12) and c.982_983insG (p.Ala328Glyfs*22) in exon eight of the AMT gene (NM_000481.4) in the proband. Genetic analysis showed that the former was inherited from the mother, and the latter was inherited from the father.

Conclusion: We report the novel compound heterozygous variation of the AMT gene in a Chinese girl with NKH by WES, which has never been reported previously. Our case expanded the AMT gene mutation spectrum, further strengthened the understanding of NKH, and deepened the genetic and clinical heterogeneity of the disease. However, the study of treatment and prognosis is still our future challenge and focus.
Prenatal Diagnosis of Chromosomal Mosaicism in Over 18,000 Pregnancies: A Five-Year Single-Tertiary-Center Retrospective Analysis
Authors: Li Shuyuan , Shi Yiru , Han Xu , Chen Yiyao , Shen Yinghua , Hu Wenjing , Zhao Xinrong , Wang Yanlin
Published: May 2022

Background: Chromosomal mosaicism (CM) is a common biological phenomenon observed in humans. It is one of the main challenges in prenatal diagnosis due to uncertain outcomes, especially when fetal ultrasonographic features appear normal. This study aimed to assess the phenotypic features of CM detected during prenatal diagnosis and the risk factors affecting parents’ pregnancy decisions.

Materials and methods: A retrospective cohort study involving 18,374 consecutive pregnancies that underwent prenatal diagnosis by karyotyping, fluorescence in situ hybridization (FISH), or chromosome microarray analysis (CMA) was conducted. The association of risk factors with malformations detected by ultrasound and pregnancy outcomes was assessed using the chi-square test and binary logistic regression. Discordant results between the different methods were identified and further analyzed.

Results: During this five-year period, 118 (0.6%) patients were diagnosed with CM. The incidences of CM in the chorionic villus, amniotic fluid, and umbilical cord blood were 3.2, 0.5, and 0.7%, respectively. The frequency of ultrasound malformations in individuals with a high fraction of autosomal CM was significantly higher than that in other groups (62.5% vs. 21.4–33.3%, all p <0.05). Inconsistent results between karyotyping and CMA/FISH were observed in 23 cases (19.5%). The risk of pregnancy termination in cases with ultrasound malformations, consistent results, autosomal CM, or a high CM fraction increased with an odds ratio of 3.09, 8.35, 2.30, and 7.62 (all p <0.05). Multiple regression analysis revealed that all four factors were independent risk factors for the termination of pregnancy.

Conclusion: Patients with a high fraction of autosomal CM are more likely to have ultrasound malformations. Inconsistent results between different methods in CM are not rare. Ultrasound malformations, consistent results between different methods, autosomal CM, and a high CM fraction were independent risk factors for the choice to terminate pregnancies.
Multi-Size Deep Learning Based Preoperative Computed Tomography Signature for Prognosis Prediction of Colorectal Cancer
Authors: Li Cheng-Hang , Cai Du , Zhong Min-Er , Lv Min-Yi , Huang Ze-Ping , Zhu Qiqi , Hu Chuling , Qi Haoning , Wu Xiaojian , Gao Feng
Published: May 2022

Background: Preoperative and postoperative evaluation of colorectal cancer (CRC) patients is crucial for subsequent treatment guidance. Our study aims to provide a timely and rapid assessment of the prognosis of CRC patients with deep learning according to non-invasive preoperative computed tomography (CT) and explore the underlying biological explanations.

Methods: A total of 808 CRC patients with preoperative CT (development cohort: n = 426, validation cohort: n = 382) were enrolled in our study. We proposed a novel end-to-end Multi-Size Convolutional Neural Network (MSCNN) to predict the risk of CRC recurrence with CT images (CT signature). The prognostic performance of CT signature was evaluated by Kaplan-Meier curve. An integrated nomogram was constructed to improve the clinical utility of CT signature by combining with other clinicopathologic factors. Further visualization and correlation analysis for CT deep features with paired gene expression profiles were performed to reveal the molecular characteristics of CRC tumors learned by MSCNN in radiographic imaging.

Results: The Kaplan-Meier analysis showed that CT signature was a significant prognostic factor for CRC disease-free survival (DFS) prediction [development cohort: hazard ratio (HR): 50.7, 95% CI: 28.4–90.6, p < 0.001; validation cohort: HR: 2.04, 95% CI: 1.44–2.89, p < 0.001]. Multivariable analysis confirmed the independence prognostic value of CT signature (development cohort: HR: 30.7, 95% CI: 19.8–69.3, p < 0.001; validation cohort: HR: 1.83, 95% CI: 1.19–2.83, p = 0.006). Dimension reduction and visualization of CT deep features demonstrated a high correlation with the prognosis of CRC patients. Functional pathway analysis further indicated that CRC patients with high CT signature presented down-regulation of several immunology pathways. Correlation analysis found that CT deep features were mainly associated with activation of metabolic and proliferative pathways.

Conclusions: Our deep learning based preoperative CT signature can effectively predict prognosis of CRC patients. Integration analysis of multi-omic data revealed that some molecular characteristics of CRC tumor can be captured by deep learning in CT images.
The Landscape of the Tumor-Infiltrating Immune Cell and Prognostic Nomogram in Colorectal Cancer
Authors: Zhong Jiateng , Qin Yu , Yu Pei , Xia Weiyue , Gu Baoru , Qian Xinlai , Hu Yuhan , Su Wei , Zhang Zheying
Published: May 2022

Tumor-infiltrating immune cells are associated with prognosis and immunotherapy targets in colorectal cancer (CRC). The recently developed CIBERSORT method allows immune cell analysis by deconvolution of high-throughput data onto gene expression. In this study, we analyzed the relative proportions of immune cells in GEO (94 samples) and TCGA (522 samples) CRC data based on the CIBERSORT method. A total of 22 types of tumor-infiltrating immune cells were evaluated. Combined with GEO and TCGA data, it was found that naive B cells, M2 macrophages, and resting mast cells were highly expressed in normal tissues, while M0 macrophages, M1 macrophages, activated mast cells, and neutrophils were highly expressed in tumors. Moreover, we constructed a prognostic model by infiltrating immune cells that showed high specificity and sensitivity in both the training (AUC of 5-year survival = 0.699) and validation (AUC of 5-year survival = 0.844) sets. This provides another basis for clinical prognosis. The results of multiple immunofluorescence detection showed that there were differences in the results of bioinformatics analysis. Neutrophils were highly expressed in normal tissues, and M2 macrophages were highly expressed in tumor tissues. Collectively, our data suggested that infiltrating immune cells in CRC may be an important determinant of prognosis and immunotherapy.
Identification of Two m6A Readers YTHDF1 and IGF2BP2 as Immune Biomarkers in Head and Neck Squamous Cell Carcinoma
Authors: Li Shaojie , Wu Qiuji , Liu Jia , Zhong Yahua
Published: May 2022

Background: N6-methyladenosine (m6A) is the most abundant internal modification pattern in mammals that a plays critical role in tumorigenesis and immune regulations. However, the effect of m6A modification on head and neck squamous cell carcinoma (HNSCC) has not been clearly studied.

Methods: We screened m6A regulators that were significantly correlated with tumor immune status indicated by ImmuneScore using The Cancer Genome Atlas (TCGA) dataset and obtained distinct patient clusters based on the expression of these m6A regulators with the R package “CensusClusterPlus.” We then performed gene set enrichment analysis (GSEA), CIBERSORT, and single-sample gene set enrichment analysis (ssGSEA) to assess the differences in gene function enrichment and tumor immune microenvironment (TIME) among these clusters. We further conducted differently expressed gene (DEG) analysis and weighted gene co-expression network analysis (WGCNA) and constructed a protein–protein interaction (PPI) network to determine hub genes among these clusters. Finally, we used the GSE65858 dataset as an external validation cohort to confirm the immune profiles related to the expression of m6A regulators.

Results: Two m6A readers, YTHDF1 and IGF2BP2, were found to be significantly associated with distinct immune status in HNSCC. Accordingly, patients were divided into two clusters with Cluster 1 showing high expression of YTHDF1 and IGF2BP2 and Cluster 2 showing low expression levels of both genes. Clinicopathologically, patients from Cluster 1 had more advanced T stage and pathological grades than those from Cluster 2. GSEA showed that Cluster 1 was closely related to the RNA modification process and Cluster 2 was significantly correlated with immune regulations. Cluster 2 had a more active TIME characterized by a more relative abundance of CD8+ T cells and CD4+ T cells and higher levels of MHC I and MHC II molecules. We constructed a PPI network composed of 16 hub genes between the two clusters, which participated in the T-cell receptor signaling pathway. These results were externally validated in the GSE65858 dataset.

Conclusions: The m6A readers, YTHDF1 and IGF2BP2, were potential immune biomarkers in HNSCC and could be potential treatment targets for cancer immunotherapy.
Identification of Immunodominant Antigens From a First-Generation Vaccine Against Cutaneous Leishmaniasis
Authors: Germanó María José , Mackern-Oberti Juan Pablo , Vitório Jessica Gardone , Duarte Mariana Costa , Pimenta Daniel Carvalho , Sanchez Maria Victoria , Bruna Flavia Alejandra , Lozano Esteban Sebastián , Fernandes Ana Paula , Cargnelutti Diego Esteban
Published: May 2022

Leishmaniasis is a neglected tropical disease (NTD) caused by parasites belonging to the Leishmania genus for which there is no vaccine available for human use. Thus, the aims of this study are to evaluate the immunoprotective effect of a first-generation vaccine against L. amazonensis and to identify its immunodominant antigens. BALB/c mice were inoculated with phosphate buffer sodium (PBS), total L. amazonensis antigens (TLAs), or TLA with Poly (I:C) and Montanide ISA 763. The humoral and cellular immune response was evaluated before infection. IgG, IgG1, and IgG2a were measured on serum, and IFN-γ, IL-4, and IL-10 cytokines as well as cell proliferation were measured on a splenocyte culture from vaccinated mice. Immunized mice were challenged with 104 infective parasites of L. amazonensis on the footpad. After infection, the protection provided by the vaccine was analyzed by measuring lesion size, splenic index, and parasite load on the footpad and spleen. To identify immunodominant antigens, total proteins of L. amazonensis were separated on 2D electrophoresis gel and transferred to a membrane that was incubated with serum from immunoprotected mice. The antigens recognized by the serum were analyzed through a mass spectrometric assay (LC-MS/MS-IT-TOF) to identify their protein sequence, which was subjected to bioinformatic analysis. The first-generation vaccine induced higher levels of antibodies, cytokines, and cell proliferation than the controls after the second dose. Mice vaccinated with TLA + Poly (I:C) + Montanide ISA 763 showed less footpad swelling, a lower splenic index, and a lower parasite load than the control groups (PBS and TLA). Four immunodominant proteins were identified by mass spectrometry: cytosolic tryparedoxin peroxidase, an uncharacterized protein, a kinetoplast-associated protein-like protein, and a putative heat-shock protein DNAJ. The identified proteins showed high levels of conserved sequence among species belonging to the Leishmania genus and the Trypanosomatidae family. These proteins also proved to be phylogenetically divergent to human and canine proteins. TLA + Poly (I:C) + Montanide ISA 763 could be used as a first-generation vaccine against leishmaniasis. The four proteins identified from the whole-protein vaccine could be good antigen candidates to develop a new-generation vaccine against leishmaniasis.
Human Macrophages Exhibit GM-CSF Dependent Restriction of Mycobacterium tuberculosis Infection via Regulating Their Self-Survival, Differentiation and Metabolism
Authors: Mishra Abhishek , Singh Vipul K. , Jagannath Chinnaswamy , Subbian Selvakumar , Restrepo Blanca I. , Gauduin Marie-Claire , Khan Arshad
Published: May 2022

GM-CSF is an important cytokine that regulates the proliferation of monocytes/macrophages and its various functions during health and disease. Although growing evidences support the notion that GM-CSF could play a major role in immunity against tuberculosis (TB) infection, the mechanism of GM-CSF mediated protective effect against TB remains largely unknown. Here in this study we examined the secreted levels of GM-CSF by human macrophages from different donors along with the GM-CSF dependent cellular processes that are critical for control ofM. tuberculosisinfection. While macrophage of different donors varied in their ability to produce GM-CSF, a significant correlation was observed between secreted levels of GM-CSF, survial of macrophages and intra-macrophage control ofMycobacterium tuberculosisbacilli. GM-CSF levels secreted by macrophages negatively correlated with the intra-macrophageM. tuberculosisburden, survival of infected host macrophages positively correlated with their GM-CSF levels. GM-CSF-dependent prolonged survival of human macrophages also correlated with significantly decreased bacterial burden and increased expression of self-renewal/cell-survival associated genes such asBCL-2andHSP27. Antibody-mediated depletion of GM-CSF in macrophages resulted in induction of significantly elevated levels of apoptotic/necrotic cell death and a simultaneous decrease in autophagic flux. Additionally, protective macrophages againstM. tuberculosisthat produced more GM-CSF, induced a stronger granulomatous response and produced significantly increased levels of IL-1β, IL-12 and IL-10 and decreased levels of TNF-α and IL-6. In parallel, macrophages isolated from the peripheral blood of active TB patients exhibited reduced capacity to control the intracellular growth ofM. tuberculosisand produced significantly lower levels of GM-CSF. Remarkably, as compared to healthy controls, macrophages of active TB patients exhibited significantly altered metabolic state correlating with their GM-CSF secretion levels. Altogether, these results suggest that relative levels of GM-CSF produced by human macrophages plays a critical role in preventing cell death and maintaining a protective differentiation and metabolic state of the host cell againstM. tuberculosisinfection.
Macrophage Cx43 Is Necessary for Fibroblast Cytosolic Calcium and Lung Fibrosis After Injury
Authors: Bhattacharyya Aritra , Torre Paola , Yadav Preeti , Boostanpour Kaveh , Chen Tian Y. , Tsukui Tatsuya , Sheppard Dean , Muramatsu Rieko , Seed Robert I. , Nishimura Stephen L. , Jung James B. , Tang Xin-Zi , Allen Christopher D. C. , Bhattacharya Mallar
Published: May 2022

Macrophages are paracrine signalers that regulate tissular responses to injury through interactions with parenchymal cells. Connexin hemichannels have recently been shown to mediate efflux of ATP by macrophages, with resulting cytosolic calcium responses in adjacent cells. Here we report that lung macrophages with deletion of connexin 43 (MacΔCx43) had decreased ATP efflux into the extracellular space and induced a decreased cytosolic calcium response in co-cultured fibroblasts compared to WT macrophages. Furthermore, MacΔCx43 mice had decreased lung fibrosis after bleomycin-induced injury. Interrogating single cell data for human and mouse, we found that P2rx4 was the most highly expressed ATP receptor and calcium channel in lung fibroblasts and that its expression was increased in the setting of fibrosis. Fibroblast-specific deletion of P2rx4 in mice decreased lung fibrosis and collagen expression in lung fibroblasts in the bleomycin model. Taken together, these studies reveal a Cx43-dependent profibrotic effect of lung macrophages and support development of fibroblast P2rx4 as a therapeutic target for lung fibrosis.
Upregulating Human Cathelicidin Antimicrobial Peptide LL-37 Expression May Prevent Severe COVID-19 Inflammatory Responses and Reduce Microthrombosis
Authors: Aloul Karim M. , Nielsen Josefine Eilsø , Defensor Erwin B. , Lin Jennifer S. , Fortkort John A. , Shamloo Mehrdad , Cirillo Jeffrey D. , Gombart Adrian F. , Barron Annelise E.
Published: May 2022

COVID-19 is characterized by hyperactivation by inflammatory cytokines and recruitment of macrophages, neutrophils, and other immune cells, all hallmarks of a strong inflammatory response that can lead to severe complications and multi-organ damage. Mortality in COVID-19 patients is associated with a high prevalence of neutrophil extracellular trap (NET) formation and microthrombosis that are exacerbated by hyperglycemia, diabetes, and old age. SARS-CoV-2 infection in humans and non-human primates have revealed long-term neurological consequences of COVID-19, possibly concomitant with the formation of Lewy bodies in the brain and invasion of the nervous system via the olfactory bulb. In this paper, we review the relevance of the human cathelicidin LL-37 in SARS-CoV-2 infections. LL-37 is an immunomodulatory, host defense peptide with direct anti-SARS-CoV-2 activity, and pleiotropic effects on the inflammatory response, neovascularization, Lewy body formation, and pancreatic islet cell function. The bioactive form of vitamin D and a number of other compounds induce LL-37 expression and one might predict its upregulation, could reduce the prevalence of severe COVID-19. We hypothesize upregulation of LL-37 will act therapeutically, facilitating efficient NET clearance by macrophages, speeding endothelial repair after inflammatory tissue damage, preventing α-synuclein aggregation, and supporting blood-glucose level stabilization by facilitating insulin release and islet β-cell neogenesis. In addition, it has been postulated that LL-37 can directly bind the S1 domain of SARS-CoV-2, mask angiotensin converting enzyme 2 (ACE2) receptors, and limit SARS-CoV-2 infection. Purposeful upregulation of LL-37 could also serve as a preventative and therapeutic strategy for SARS-CoV-2 infections.
Sex-Biased Control of Inflammation and Metabolism by a Mitochondrial Nod-Like Receptor
Authors: Snäkä Tiia , Bekkar Amel , Desponds Chantal , Prével Florence , Claudinot Stéphanie , Isorce Nathalie , Teixeira Filipa , Grasset Coline , Xenarios Ioannis , Lopez-Mejia Isabel C. , Fajas Lluis , Fasel Nicolas
Published: May 2022

Mitochondria regulate steroid hormone synthesis, and in turn sex hormones regulate mitochondrial function for maintaining cellular homeostasis and controlling inflammation. This crosstalk can explain sex differences observed in several pathologies such as in metabolic or inflammatory disorders. Nod-like receptor X1 (NLRX1) is a mitochondria-associated innate receptor that could modulate metabolic functions and attenuates inflammatory responses. Here, we showed that in an infectious model with the human protozoan parasite,Leishmania guyanensis, NLRX1 attenuated inflammation in females but not in male mice. Analysis of infected female and male bone marrow derived macrophages showed both sex- and genotype-specific differences in both inflammatory and metabolic profiles with increased type I interferon production, mitochondrial respiration, and glycolytic rate inNlrx1-deficient female BMDMs in comparison to wild-type cells, while no differences were observed between males. Transcriptomics of female and male BMDMs revealed an altered steroid hormone signaling inNlrx1-deficient cells, and a “masculinization” ofNlrx1-deficient female BMDMs. Thus, our findings suggest that NLRX1 prevents uncontrolled inflammation and metabolism in females and therefore may contribute to the sex differences observed in infectious and inflammatory diseases.
SARS-CoV-2-mRNA Booster Vaccination Reverses Non-Responsiveness and Early Antibody Waning in Immunocompromised Patients – A Phase Four Study Comparing Immune Responses in Patients With Solid Cancers, Multiple Myeloma and Inflammatory Bowel Disease
Authors: Wagner Angelika , Garner-Spitzer Erika , Schötta Anna-Margarita , Orola Maria , Wessely Andrea , Zwazl Ines , Ohradanova-Repic Anna , Weseslindtner Lukas , Tajti Gabor , Gebetsberger Laura , Kratzer Bernhard , Tomosel Elena , Kutschera Maximilian , Tobudic Selma , Pickl Winfried F. , Kundi Michael , Stockinger Hannes , Novacek Gottfried , Reinisch Walter , Zielinski Christoph , Wiedermann Ursula
Published: May 2022

Background

Individuals with secondary immunodeficiencies belong to the most vulnerable groups to succumb to COVID-19 and thus are prioritized for SARS-CoV-2 vaccination. However, knowledge about the persistence and anamnestic responses following SARS-CoV-2-mRNA vaccinations is limited in these patients.

Methods

In a prospective, open-label, phase four trial we analyzed S1-specific IgG, neutralizing antibodies and cytokine responses in previously non-infected patients with cancer or autoimmune disease during primary mRNA vaccination and up to one month after booster.

Results

263 patients with solid tumors (SOT, n=63), multiple myeloma (MM, n=70), inflammatory bowel diseases (IBD, n=130) and 66 controls were analyzed. One month after the two-dose primary vaccination the highest non-responder rate was associated with lower CD19+ B-cell counts and was found in MM patients (17%). S1-specific IgG levels correlated with IL-2 and IFN-γ responses in controls and IBD patients, but not in cancer patients. Six months after the second dose, 18% of patients with MM, 10% with SOT and 4% with IBD became seronegative; no one from the control group became negative. However, in IBD patients treated with TNF-α inhibitors, antibody levels declined more rapidly than in controls. Overall, vaccination with mRNA-1273 led to higher antibody levels than with BNT162b2. Importantly, booster vaccination increased antibody levels >8-fold in seroresponders and induced anamnestic responses even in those with undetectable pre-booster antibody levels. Nevertheless, in IBD patients with TNF-α inhibitors even after booster vaccination, antibody levels were lower than in untreated IBD patients and controls.

Conclusion

Immunomonitoring of vaccine-specific antibody and cellular responses seems advisable to identify vaccination failures and consequently establishing personalized vaccination schedules, including shorter booster intervals, and helps to improve vaccine effectiveness in all patients with secondary immunodeficiencies.

Trial registration

EudraCT Number: 2021-000291-11
Time-Dependent Increase in Susceptibility and Severity of Secondary Bacterial Infections During SARS-CoV-2
Authors: Smith Amanda P. , Williams Evan P. , Plunkett Taylor R. , Selvaraj Muneeswaran , Lane Lindey C. , Zalduondo Lillian , Xue Yi , Vogel Peter , Channappanavar Rudragouda , Jonsson Colleen B. , Smith Amber M.
Published: May 2022

Secondary bacterial infections can exacerbate SARS-CoV-2 infection, but their prevalence and impact remain poorly understood. Here, we established that a mild to moderate infection with the SARS-CoV-2 USA-WA1/2020 strain increased the risk of pneumococcal (type 2 strain D39) coinfection in a time-dependent, but sex-independent, manner in the transgenic K18-hACE2 mouse model of COVID-19. Bacterial coinfection increased lethality when the bacteria was initiated at 5 or 7 d post-virus infection (pvi) but not at 3 d pvi. Bacterial outgrowth was accompanied by neutrophilia in the groups coinfected at 7 d pvi and reductions in B cells, T cells, IL-6, IL-15, IL-18, and LIF were present in groups coinfected at 5 d pvi. However, viral burden, lung pathology, cytokines, chemokines, and immune cell activation were largely unchanged after bacterial coinfection. Examining surviving animals more than a week after infection resolution suggested that immune cell activation remained high and was exacerbated in the lungs of coinfected animals compared with SARS-CoV-2 infection alone. These data suggest that SARS-CoV-2 increases susceptibility and pathogenicity to bacterial coinfection, and further studies are needed to understand and combat disease associated with bacterial pneumonia in COVID-19 patients.
Activation and Regulation of NLRP3 by Sterile and Infectious Insults
Authors: Banerjee Srijon K. , Chatterjee Ayan , Gupta Shamba , Nagar Abhinit
Published: May 2022

Nod-Like Receptor (NLR) is the largest family of Pathogen Recognition Receptors (PRRs) that patrols the cytosolic environment. NLR engagement drives caspase-1 activation that cleaves pro-IL-1B which then gets secreted. Released IL-1B recruits immune cells to the site of infection/injury. Caspase-1 also cleaves Gasdermin-D (GSDM-D) that forms pores within the plasma membrane driving inflammatory cell death called pyroptosis. NLRP3 is the most extensively studied NLR. The NLRP3 gene is encoded by 9 exons, where exon 1 codes for pyrin domain, exon 3 codes for NACHT domain, and Leucine Rich Repeat (LRR) domain is coded by exon 4-9. Exon 2 codes for a highly disorganized loop that connects the rest of the protein to the pyrin domain and may be involved in NLRP3 regulation. The NLRP3 inflammasome is activated by many structurally divergent agonists of microbial, environmental, and host origin. Activated NLRP3 interacts with an adaptor protein, ASC, that bridges it to pro-Caspase-1 forming a multi-protein complex called inflammasome. Dysregulation of NLRP3 inflammasome activity is a hallmark of pathogenesis in several human diseases, indicating its highly significant clinical relevance. In this review, we summarize the existing knowledge about the mechanism of activation of NLRP3 and its regulation during activation by infectious and sterile triggers.
Advances on Innate Immune Evasion by Avian Immunosuppressive Viruses
Authors: Wang Hongnuan , Li Wei , Zheng Shijun J.
Published: May 2022

Innate immunity is not only the first line of host defense against pathogenic infection, but also the cornerstone of adaptive immune response. Upon pathogenic infection, pattern recognition receptors (PRRs) of host engage pathogen-associated molecular patterns (PAMPs) of pathogens, which initiates IFN production by activating interferon regulatory transcription factors (IRFs), nuclear factor-kappa B (NF-κB), and/or activating protein-1 (AP-1) signal transduction pathways in host cells. In order to replicate and survive, pathogens have evolved multiple strategies to evade host innate immune responses, including IFN-I signal transduction, autophagy, apoptosis, necrosis, inflammasome and/or metabolic pathways. Some avian viruses may not be highly pathogenic but they have evolved varied strategies to evade or suppress host immune response for survival, causing huge impacts on the poultry industry worldwide. In this review, we focus on the advances on innate immune evasion by several important avian immunosuppressive viruses (infectious bursal disease virus (IBDV), Marek’s disease virus (MDV), avian leukosis virus (ALV), etc.), especially their evasion of PRRs-mediated signal transduction pathways (IFN-I signal transduction pathway) and IFNAR-JAK-STAT signal pathways. A comprehensive understanding of the mechanism by which avian viruses evade or suppress host immune responses will be of help to the development of novel vaccines and therapeutic reagents for the prevention and control of infectious diseases in chickens.
Applying Tissue Separation and Untargeted Metabolomics to Understanding Lipid Saturation Kinetics of Host Mitochondria and Symbiotic Algae in Corals Under High Temperature Stress
Authors: Gamba Andrea , Petras Daniel , Little Mark , White Brandie , Dorrestein Pieter C. , Rohwer Forest , Foster Rachel A. , Hartmann Aaron C.
Published: May 2022

Untargeted metabolomics is a powerful tool for profiling the biochemical phenotypes of organisms and discovering new metabolites that drive biological function and might be exploited as pharmaceutical leads. Yet, connecting physiological processes to metabolites detected remains a challenge due to the lack of structural and activity annotations and the underlying complexity of mixed samples (e.g., multiple microorganisms, organelles, etc.). To simplify this biological complexity, we separated coral holobionts into host mitochondria and their algal symbionts prior to LC-MS/MS-based untargeted metabolomic analysis followed by molecular networking. We found distinct metabolomic profiles between tissue fractions. Notably, 14% of metabolites detected were only observed in the mitochondria and algal symbionts, not in the holobiont, and thus were masked when the bulk (holobiont) sample was analyzed. The utility of tissue separation for hypothesis testing was assessed using a simple temperature experiment. We tested the hypothesis that membrane lipids of the coral mitochondria and algal symbionts become more saturated at higher temperatures to maintain membrane rigidity. While the holobiont metabolite profiles showed little change in response to elevated temperature, there was a change in lipid saturation of both fractions through time. The fatty acid saturation of both the coral mitochondria and the algal symbionts shifted upon exposure to higher temperatures (1 h) then returned to ambient saturation levels by 4 h, indicating rapid acclimatization to warmer water. Surprisingly, the fractions deviated in opposite directions: during the first hour of the experiment, the mitochondria showed an increase in saturated lipid concentrations, while the algal symbionts showed an increase in unsaturated lipids. Partitioning the holobiont prior to untargeted metabolomic analysis revealed disparate responses to environmental stress that would have gone undetected if only the holobiont/bulk tissue was analyzed. This work illustrates rapid physiological acclimatization to environmental changes in specific host organelles and symbionts, though via different paths.
The Effects of Hurricanes and Storms on the Composition of Dissolved Organic Matter in a Southeastern U.S. Estuary
Authors: Medeiros Patricia M.
Published: May 2022

Extreme events such as hurricanes and tropical storms often result in large fluxes of dissolved organic carbon (DOC) to estuaries. Precipitation associated with tropical storms may be increasing in the southeastern U.S., which can potentially impact dissolved organic matter (DOM) dynamics and cycling in coastal systems. Here, DOM composition at the Altamaha River and Estuary (Georgia, U.S.A.) was investigated over multiple years capturing seasonal variations in river discharge, high precipitation events, and the passage of two hurricanes which resulted in substantial storm surges. Optical measurements of DOM indicate that the terrigenous signature in the estuary is linearly related to freshwater content and is similar after extreme events with or without a storm surge and during peak river flow. Molecular level analysis revealed significant differences, however, with a large increase of highly aromatic compounds after extreme events exceeding what would be expected by freshwater content alone. Although extreme events are often followed by increased DOC biodegradation, the terrigenous material added during those events does not appear to be more labile than the remainder of the DOM pool that was captured by ultrahigh-resolution mass spectrometry analysis. This suggests that the added terrigenous organic matter may be exported to the coastal ocean, while a fraction of the organic matter that co-varied with the terrigenous DOM may contribute to the increased biomineralization in the estuary, with implications to carbon processing in coastal areas.
Quantifying the Influence of Out-Time on Prepreg Material Properties and Out-Of-Plane Steering Defects During Automated Fiber Placement
Authors: Heller Klaus , Colin David , Drechsler Klaus
Published: May 2022

In automated fiber placement (AFP), knowledge about the interaction between material properties and process parameters is essential to achieve cost-efficient manufacturing. Both, lay-up rate and defects are dependent on the properties of the uncured prepreg tapes which are out-time dependent. However, information thereof is not given in data sheets and there are no standardized test methods. To quantify the changes of the material properties, we conducted experiments on mechanical properties and tack with IM7/8552 up to 15 days out-time using previously evaluated test methods. Furthermore, we carried out AFP lay-up trials to quantify the effects on steering defects. The results for the mechanical properties reveal a non-linear increase of the shear modulus and the transverse tensile modulus and a strong correlation to the test temperature. Results from the probe tack tests show a strong dependence on out-time at 20°C and a weak dependence at 40°C. Results from a novel peel tack test method and the lay-up trials revealed a monotonous change as a function of out-time. In both cases, we identified the lay-up rate and the infrared (IR) emitter power as the process parameters with the largest influence. The obtained results present an overall view of the material behavior depending on different test and process parameters as a function of out-time. By this, they help optimize the AFP process parameters and serve as input for material models and AFP defect models.
A Multi-Center, Randomized, Blind, Controlled Clinical Trial of the Safety and Efficacy of Micro Radio Frequency Therapy System for the Treatment of Overactive Bladder
Authors: Xu Zhi-Hui , Zhang Peng-Fei , Wang Yu-Feng , Ma Ao , Bano Yasmeen , Ibrohimov Alisherjon , Zhang Chen , Jiang Hao-Fei , Zhang Yang , Yu Yan-Lan , Jiang Hai-Hong
Published: May 2022

Purpose

The purpose of this study was to evaluate the efficacy and safety of low power micro radiofrequency (RF) therapy (μRFthera®) through urethra in the treatment of overactive bladders (OAB) through a prospective, single-blind, placebo-controlled, multi-center clinical protocol.

Materials and Methods

One hundred and fourteen patients with refractory OAB were randomized at 2:1 ratio, treatment to control undergoing same procedures except only the micro-RF treatment group at turned “on” setting in energy. Bladder diaries recorded during the screening period (3 days before enrollment) and during follow-up period on week 1, 3, and 7, respectively. The patients in control could choose receiving an energized treatment during extension stage.

Results

The treatment efficacy was 76.1%. There was 49.80% rate improvement compared to control (95%CL 32.48%, 67.13%). The crude rate ration (RR) was 2.89, 95% CI (1.67–5.01) with p < 0.001 in uni-variate analysis, while the RR became 2.94, 95% CI (1.67–5.16) with p < 0.001 after adjusted potential confounding factors in multi-variate analysis. Statistically significant improvements have been demonstrated in the frequency of urination, urgency, nocturia, and quality of life (QoL) scores.

Conclusions

Micro RF therapy is safe and effective for the treatment of OAB. The main treatment-related complications were catheterization related complications.

Clinical Trial Registration

Zhejiang Device Registration Certificate No. 202090909, www.chictr.org.cn, Clinical Trial Accession Number: ChiCTR2100050096.
Arterial Stiffness and Adult Onset Vasculitis: A Systematic Review
Authors: Lo Gullo Alberto , Giuffrida Clemente , Morace Carmela , Squadrito Giovanni , Magnano San Lio Paola , Ricciardi Luisa , Salvarani Carlo , Mandraffino Giuseppe
Published: May 2022

Chronic inflammation represents the cornerstone of the raised cardiovascular (CV) risk in patients with inflammatory rheumatic diseases (IRD), including vasculitis. Standardized mortality ratios in these patients are higher as compared to the general population, and the excess of premature mortality is due to early atherosclerotic events. Thus, IRD patients need appropriate CV risk assessment and management according to this CV disease (CVD) burden. Adequate control of CV risk is still lacking in usual care, but early diagnosis of silent and subclinical CVD is crucial to improve the long-term prognosis of these patients. Increased arterial stiffness may provide a pathophysiological link between inflammation and increased cardiovascular risk. Several noninvasive methods are now available to estimate artery stiffness in the clinical setting, including pulse wave velocity assessment. The independent predictive value of arterial stiffness for cardiovascular events has been demonstrated in general as well as in selected populations, and reference values adjusted for age and blood pressure have been suggested. Thus, arterial stiffness is an interesting biomarker for cardiovascular risk stratification. This systematic review summarizes the additional value that PWV measurement can provide in the setting of vasculitis, with a focus in the different clinical stages and CV risk prevention. This systematic review is registered with registration number: Prospero CRD42021259603.
The BASDAI Cut-Off for Disease Activity Corresponding to the ASDAS Scores in a Taiwanese Cohort of Ankylosing Spondylitis
Authors: Chen Yi-Hsing , Huang Wen-Nan , Chen Yi-Ming , Lai Kuo-Lung , Hsieh Tsu-Yi , Hung Wei-Ting , Lin Ching-Tsai , Tseng Chih-Wei , Tang Kuo-Tung , Chou Yin-Yi , Wu Yi-Da , Huang Chin-Yin , Hsieh Chia-Wei , Chen Yen-Ju , Liao Yu-Wan , Chen Hsin-Hua
Published: May 2022

Objectives

The Bath Ankylosing Spondylitis Disease Activity Index (BASDAI) has been widely utilized to evaluate disease activity in patients with ankylosing spondylitis (AS) by an arbitrary cut-off of ≥4 to indicate high disease activity and initiate biological therapy. The Ankylosing Spondylitis Disease Activity Score (ASDAS) is a new composite index to assess AS disease activity states that have been defined and validated. ASDAS ≥2.1 was selected as a criterion to start biological therapy. The purpose of this study was to estimate the corresponding BASDAI and ASDAS cut-off in a Taiwanese AS cohort.

Methods

From November 2016 to October 2018, we assessed the ASDAS and the BASDAI regularly and recorded demographic data for 489 AS patients in Taichung Veterans General hospital (TCVGH) using an electronic patient-reported data system linked to electronic medical records. We used receiver operating characteristic curves with Youden's J statistic to determine the BASDAI values that correspond to ASDAS disease activity cut-offs (i.e., 1.3, 2.1, and 3.5).

Results

In our population, the best trade-off BASDAI values corresponding to ASDAS -C-reactive protein (CRP) 1.3, 2.1, and 3.5 were 2.1, 3.1, and 3.7, respectively. The optimal BASDAI values corresponding to ASDAS-erythrocyte sedimentation rates 1.3, 2.1, and 3.5 were 2.0, 2.6, and 4.8, respectively.

Conclusion

We propose a revised BASDAI cut-off based on our data, as BASDAI scores are commonly used globally. A more reasonable, lower BASDAI cut-off to initiate or change biological therapy will bring us closer to better decisions to treat AS patients.
Increase in Serum Soluble Tim-3 Level Is Related to the Progression of Diseases After Hepatitis Virus Infection
Authors: Chen Lingli , Yu Xiaomei , Lv Chunyan , Dai Yaping , Wang Tao , Zheng Shaoxiong , Qin Yuan , Zhou Xiumei , Wang Yigang , Pei Hao , Fang Hongming , Huang Biao
Published: May 2022

Background

Viral hepatitis is a widespread and serious infectious disease, and most patients with liver cirrhosis and hepatocellular carcinoma are prone to viral infections. T cell immunoglobulin-and mucin-domain-containing molecule-3 (Tim-3) is an immune checkpoint molecule that negatively regulates T cell responses, playing an extremely important role in controlling infectious diseases. However, reports about the role of serum soluble Tim-3 (sTim-3) in hepatitis virus infection are limited. Therefore, this study explored changes in sTim-3 levels in patients infected with hepatitis B virus (HBV), hepatitis C virus (HCV), and hepatitis E virus (HEV).

Methods

This study applied high-sensitivity time-resolved fluorescence immunoassay for the detection of sTim-3 levels. A total of 205 cases of viral hepatitis infection (68 cases of HBV infection, 60 cases of HCV infection, and 77 cases of HEV virus infection) and 88 healthy controls were quantitatively determined. The changes in serum sTim-3 level and its clinical value in hepatitis virus infection were analyzed.

Results

Patients with HBV infection (14.00, 10.78–20.45 ng/mL), HCV infection (15.99, 11.83–27.00 ng/mL), or HEV infection (19.09, 10.85–33.93 ng/mL) had significantly higher sTim-3 levels than that in the healthy control group (7.69, 6.14–10.22 ng/mL, P < 0.0001). Patients with hepatitis and fibrosis infected with HBV (22.76, 12.82–37.53 ng/mL), HCV (33.06, 16.36–39.30 ng/mL), and HEV (28.90, 17.95–35.94 ng/mL) had significantly higher sTim-3 levels than patients with hepatitis without fibrosis (13.29, 7.75–17.28; 13.86, 11.48–18.64; 14.77, 9.79–29.79 ng/mL; P < 0.05).

Conclusion

sTim-3 level was elevated in patients infected with HBV, HCV, or HEV and gradually increased in patients with either hepatitis or hepatitis with hepatic fibrosis. It has a certain role in the evaluation of the course of a disease after hepatitis virus infection.
Preliminary Investigation of the Biomarkers of Acute Renal Transplant Rejection Using Integrated Proteomics Studies, Gene Expression Omnibus Datasets, and RNA Sequencing
Authors: Han Shuai , Zhao Wenjun , Wang Cuili , Wang Yucheng , Song Rong , Haller Hermann , Jiang Hong , Chen Jianghua
Published: May 2022

A kidney transplant is often the best treatment for end-stage renal disease. Although immunosuppressive therapy sharply reduces the occurrence of acute allograft rejection (AR), it remains the main cause of allograft dysfunction. We aimed to identify effective biomarkers for AR instead of invasive kidney transplant biopsy. We integrated the results of several proteomics studies related to AR and utilized public data sources. Gene ontology (GO) and pathway analyses were used to identify important biological processes and pathways. The performance of the identified proteins was validated using several public gene expression omnibus (GEO) datasets. Samples that performed well were selected for further validation through RNA sequencing of peripheral blood mononuclear cells of patients with AR (n = 16) and non-rejection (n = 19) from our medical center. A total of 25 differentially expressed proteins (DEPs) overlapped in proteomic studies of urine and blood samples. GO analysis showed that the DEPs were mainly involved in the immune system and blood coagulation. Pathway analysis showed that the complement and coagulation cascade pathways were well enriched. We found that immunoglobulin heavy constant alpha 1 (IGHA1) and immunoglobulin κ constant (IGKC) showed good performance in distinguishing AR from non-rejection groups validated with several GEO datasets. Through RNA sequencing, the combination of IGHA1, IGKC, glomerular filtration rate, and donor age showed good performance in the diagnosis of AR with ROC AUC 91.4% (95% CI: 82–100%). Our findings may contribute to the discovery of potential biomarkers for AR monitoring.