bluuebunny/crossref_metadata_2025 huggingface dataset:
Keratin 17 Is Required for Lipid Metabolism in Keratinocytes and Benefits Epidermal Permeability Barrier Homeostasis
Authors: Pang Bingyu , Zhu Zhenlai , Xiao Chunying , Luo Yixin , Fang Hui , Bai Yaxing , Sun Zhongbin , Ma Jingyi , Dang Erle , Wang Gang
Published: January 2022

The epidermal barrier refers to the stratum corneum, the uppermost layer of the skin, and constitutes the first line of defense against invasion by potentially harmful pathogens, diminishes trans-epidermal water loss, and plays a crucial role in the maintenance of skin homeostasis. Keratin 17 (K17) is a type I epithelial keratin with multiple functions, including in skin inflammation, epithelial cell growth, protein synthesis, and tumorigenesis. However, the relationship between K17 and the skin barrier has yet to be systematically investigated. In this study, we found that acute disruption of the epidermal permeability barrier led to a rapid increase in epidermal K17 expression in vivo. Krt17 gene deficiency in mice resulted in decreased expression of lipid metabolism-related enzymes and antimicrobial peptides, while also delaying epidermal permeability barrier recovery after acute disruption. Adenovirus-mediated overexpression of K17 enhanced, whereas siRNA-mediated knockdown of Krt17 inhibited, the expression of fatty acid synthase (FASN) and that of the transcription factors SREBP-1 and PPARγ in vitro. We further confirmed that K17 can facilitate the nuclear transportation of SREBP-1 and PPARγ and promote lipid synthesis in keratinocytes. This study demonstrated that K17 contributes to the restoration of the epidermal permeability barrier via stabilizing lipid metabolism in keratinocytes.
Emerging Role of LncRNA Regulation for NLRP3 Inflammasome in Diabetes Complications
Authors: Lu Xiaolin , Tan Qihong , Ma Jianyong , Zhang Jing , Yu Peng
Published: January 2022

Diabetes is a widespread metabolic disease with various complications, including diabetic nephropathy, retinopathy, cardiomyopathy, and other cardiovascular or cerebrovascular diseases. As the prevalence of diabetes increases in all age groups worldwide, diabetes and its complications cause an emerging public health burden. NLRP3 inflammasome is a complex of several proteins that play a critical role in inflammatory response and various diseases, including diabetes and its complications. Accumulating evidences indicate that NLRP3 inflammasome contributes to the development of diabetes and diabetic complications and that NLRP3 inflammation inactivation is beneficial in treating these illnesses. Emerging evidences suggest the critical role of long non-coding RNAs (lncRNAs) in regulating NLRP3 inflammasome activity in various diseases. LncRNAs are non-coding RNAs exceeding 200 nucleotides in length. Its dysregulation has been linked to the development of diseases, including diabetes. Recently, growing evidences hint that regulating lncRNAs on NLRP3 inflammasome is critical in developing and progressing diabetes and diabetic complications. Here, we discuss the role of lncRNAs in regulating NLRP3 inflammasome as well as its participation in diabetes and diabetic complications, providing novel insights into developing future therapeutic approaches for diabetes.
A Novel Platelet-Related Gene Signature for Predicting the Prognosis of Triple-Negative Breast Cancer
Authors: Xie Jindong , Zou Yutian , Ye Feng , Zhao Wanzhen , Xie Xinhua , Ou Xueqi , Xie Xiaoming , Wei Weidong
Published: January 2022

Regarded as the most invasive subtype, triple-negative breast cancer (TNBC) lacks the expression of estrogen receptors (ERs), progesterone receptors (PRs), and human epidermal growth factor receptor 2 (HER2) proteins. Platelets have recently been shown to be associated with metastasis of malignant tumors. Nevertheless, the status of platelet-related genes in TNBC and their correlation with patient prognosis remain unknown. In this study, the expression and variation levels of platelet-related genes were identified and patients with TNBC were divided into three subtypes. We collected cohorts from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. By applying the least absolute shrinkage and selection operator (LASSO) Cox regression method, we constructed a seven-gene signature which classified the two cohorts of patients with TNBC into low- or high-risk groups. Patients in the high-risk group were more likely to have lower survival rates than those in the low-risk group. The risk score, incorporated with the clinical features, was confirmed as an independent factor for predicting the overall survival (OS) time. Functional enrichment analyses revealed the involvement of a variety of vital biological processes and classical cancer-related pathways that could be important to the ultimate prognosis of TNBC. We then built a nomogram that performed well. Moreover, we tested the model in other cohorts and obtained positive outcomes. In conclusion, platelet-related genes were closely related to TNBC, and this novel signature could serve as a tool for the assessment of clinical prognosis.
Complexome Profiling—Exploring Mitochondrial Protein Complexes in Health and Disease
Authors: Cabrera-Orefice Alfredo , Potter Alisa , Evers Felix , Hevler Johannes F. , Guerrero-Castillo Sergio
Published: January 2022

Complexome profiling (CP) is a state-of-the-art approach that combines separation of native proteins by electrophoresis, size exclusion chromatography or density gradient centrifugation with tandem mass spectrometry identification and quantification. Resulting data are computationally clustered to visualize the inventory, abundance and arrangement of multiprotein complexes in a biological sample. Since its formal introduction a decade ago, this method has been mostly applied to explore not only the composition and abundance of mitochondrial oxidative phosphorylation (OXPHOS) complexes in several species but also to identify novel protein interactors involved in their assembly, maintenance and functions. Besides, complexome profiling has been utilized to study the dynamics of OXPHOS complexes, as well as the impact of an increasing number of mutations leading to mitochondrial disorders or rearrangements of the whole mitochondrial complexome. Here, we summarize the major findings obtained by this approach; emphasize its advantages and current limitations; discuss multiple examples on how this tool could be applied to further investigate pathophysiological mechanisms and comment on the latest advances and opportunity areas to keep developing this methodology.
Retinal Development and Pathophysiology in Kcnj13 Knockout Mice
Authors: Jiao Xiaodong , Ma Zhiwei , Lei Jingqi , Liu Pinghu , Cai Xiaoyu , Shahi Pawan K. , Chan Chi-Chao , Fariss Robert , Pattnaik Bikash R. , Dong Lijin , Hejtmancik J. Fielding
Published: January 2022

Purpose: We constructed and characterized knockout and conditional knockout mice for KCNJ13, encoding the inwardly rectifying K+ channel of the Kir superfamily Kir7.1, mutations in which cause both Snowflake Vitreoretinal Degeneration (SVD) and Retinitis pigmentosa (RP) to further elucidate the pathology of this disease and to develop a potential model system for gene therapy trials.

Methods: A Kcnj13 knockout mouse line was constructed by inserting a gene trap cassette expressing beta-galactosidase flanked by FRT sites in intron 1 with LoxP sites flanking exon two and converted to a conditional knockout by FLP recombination followed by crossing with C57BL/6J mice having Cre driven by the VMD2 promoter. Lentiviral replacement of Kcnj13 was driven by the EF1a or VMD2 promoters.

Results: Blue-Gal expression is evident in E12.5 brain ventricular choroid plexus, lens, neural retina layer, and anterior RPE. In the adult eye expression is seen in the ciliary body, RPE and choroid. Adult conditional Kcnj13 ko mice show loss of photoreceptors in the outer nuclear layer, inner nuclear layer thinning with loss of bipolar cells, and thinning and disruption of the outer plexiform layer, correlating with Cre expression in the overlying RPE which, although preserved, shows morphological disruption. Fundoscopy and OCT show signs of retinal degeneration consistent with the histology, and photopic and scotopic ERGs are decreased in amplitude or extinguished. Lentiviral based replacement of Kcnj13 resulted in increased ERG c- but not a- or b- wave amplitudes.

Conclusion: Ocular KCNJ13 expression starts in the choroid, lens, ciliary body, and anterior retina, while later expression centers on the RPE with no/lower expression in the neuroretina. Although KCNJ13 expression is not required for survival of the RPE, it is necessary for RPE maintenance of the photoreceptors, and loss of the photoreceptor, outer plexiform, and outer nuclear layers occur in adult KCNJ13 cKO mice, concomitant with decreased amplitude and eventual extinguishing of the ERG and signs of retinitis pigmentosa on fundoscopy and OCT. Kcnj13 replacement resulting in recovery of the ERG c- but not a- and b-waves is consistent with the degree of photoreceptor degeneration seen on histology.
Sperm IZUMO1 Is Required for Binding Preceding Fusion With Oolemma in Mice and Rats
Authors: Matsumura Takafumi , Noda Taichi , Satouh Yuhkoh , Morohoshi Akane , Yuri Shunsuke , Ogawa Masaki , Lu Yonggang , Isotani Ayako , Ikawa Masahito
Published: January 2022

Fertilization occurs as the culmination of multi-step complex processes. First, mammalian spermatozoa undergo the acrosome reaction to become fusion-competent. Then, the acrosome-reacted spermatozoa penetrate the zona pellucida and adhere to and finally fuse with the egg plasma membrane. IZUMO1 is the first sperm protein proven to be essential for sperm-egg fusion in mammals, as Izumo1 knockout mouse spermatozoa adhere to but fail to fuse with the oolemma. However, the IZUMO1 function in other species remains largely unknown. Here, we generated Izumo1 knockout rats by CRISPR/Cas9 and found the male rats were infertile. Unlike in mice, Izumo1 knockout rat spermatozoa failed to bind to the oolemma. Further investigation revealed that the acrosome-intact sperm binding conceals a decreased number of the acrosome-reacted sperm bound to the oolemma in Izumo1 knockout mice. Of note, we could not see any apparent defects in the binding of the acrosome-reacted sperm to the oolemma in the mice lacking recently found fusion-indispensable genes, Fimp, Sof1, Spaca6, or Tmem95. Collectively, our data suggest that IZUMO1 is required for the sperm-oolemma binding prior to fusion at least in rat.
Application and Progress of Raman Spectroscopy in Male Reproductive System
Authors: Zhang Feng , Tan Yiling , Ding Jinli , Cao Dishuang , Gong Yanan , Zhang Yan , Yang Jing , Yin Tailang
Published: January 2022

Raman spectroscopy is a fast-developing, unmarked, non-invasive, non-destructive technique which allows for real-time scanning and sampling of biological samples in situ, reflecting the subtle biochemical composition alterations of tissues and cells through the variations of spectra. It has great potential to identify pathological tissue and provide intraoperative assistance in clinic. Raman spectroscopy has made many exciting achievements in the study of male reproductive system. In this review, we summarized literatures about the application and progress of Raman spectroscopy in male reproductive system from PubMed and Ovid databases, using MeSH terms associated to Raman spectroscopy, prostate, testis, seminal plasma and sperm. The existing challenges and development opportunities were also discussed and prospected.
Association Between Breastmilk Microbiota and Food Allergy in Infants
Authors: Wang Shuo , Wei Yuan , Liu Luyan , Li Zailing
Published: January 2022

Regulating the composition of human breastmilk has the potential to prevent allergic diseases early in life. The composition of breastmilk is complex, comprising varying levels of oligosaccharides, immunoactive molecules, vitamins, metabolites, and microbes. Although several studies have examined the relationship between different components of breastmilk and infant food allergies, few have investigated the relationship between microorganisms in breastmilk and infant food allergy. In the present study, we selected 135 healthy pregnant women and their full-term newborns from a cohort of 202 mother–infant pairs. Among them, 69 infants were exclusively breastfed until 6 mo after birth. At follow-up, 11 of the 69 infants developed a food allergy in infancy while 22 showed no signs of allergy. Thirty-three breastmilk samples were collected within 1 mo after delivery, and 123 infant fecal samples were collected at five time points following their birth. These samples were analyzed using microbial 16S rRNA gene sequencing. The abundance and evenness of the milk microbiota and the number of differential bacteria were higher in the breastmilk samples from the non-allergy group than in those from the food allergy group. The non-allergy group showed relatively high abundance of Bifidobacterium, Akkermansia, Clostridium IV, Clostridium XIVa, Veillonella, and butyrate-producing bacteria such as Fusobacterium, Lachnospiraceae incertae sedis, Roseburia, and Ruminococcus. In contrast, the abundance of Proteobacteria, Acinetobacter, and Pseudomonas in breastmilk was higher in the food allergy group. A comparison of the changes in dominant differential breastmilk microbiota in the intestinal flora of the two groups of infants over time revealed that the changes in Bifidobacterium abundance were consistent with those in the breastmilk flora. Functional pathway prediction of breastmilk microflora showed that the enhancement of the metabolic pathways of tyrosine, tryptophan, and fatty acids was significantly different between the groups. We suggest that changes in the breastmilk microbiota can influence the development of food allergies. Breastmilk contains several microbes that have protective effects against food allergies, both by influencing the colonization of intestinal microbiota and by producing butyrate. This study may provide new ideas for improving infant health through early intervention with probiotics.
Does the Use of Complex Sentences Differentiate Between Bilinguals With and Without DLD? Evidence From Conversation and Narrative Tasks
Authors: Paradis Johanne , Sorenson Duncan Tamara , Thomlinson Stephanie , Rusk Brian
Published: January 2022

Over-identification of language disorder among bilingual children with typical development (TD) is a risk factor in assessment. One strategy for improving assessment accuracy with bilingual children is to determine which linguistic sub-domains differentiate bilingual children with TD from bilingual children with developmental language disorder (DLD). To date, little research on sequential bilinguals with TD and DLD has focussed on complex (multi-clausal) sentences in naturalistic production, even though this is a noted domain of weakness for school-age monolinguals with DLD. Accordingly, we sought to determine if there were differences in the use of complex sentences in conversational and narrative tasks between school-age sequential bilinguals with TD and with DLD at the early stages of L2 acquisition. We administered a conversation and a narrative task to 63 English L2 children with TD and DLD, aged 5–7 years with 2 years of exposure to the L2. Children had diverse first language backgrounds. The L2-TD and L2-DLD groups were matched for age, length of L2 exposure and general L2 proficiency (receptive vocabulary size). Language samples from both tasks were coded and analyzed for the use of complex versus simple sentences, for the distribution of complex sentence types, for clausal density and mean length of utterance (MLU). Complex sentences included coordinated clauses, sentential complement clauses, adverbial clauses and relative clauses. Using regression modelling and PERMANOVA, we found that the L2-TD group produced more complex sentences than the L2-DLD group, with coordinated clauses, adverbial clauses and relative clauses differing the most between the groups. Furthermore, the two groups differed for mean clausal density, but not for MLU, indicating that clausal density and MLU did not estimate identical morphosyntactic abilities. Individual variation in complex sentence production for L2-TD was predicted by longer L2 exposure and task; by contrast, for L2-DLD, it was predicted by older age. This study indicates that complex sentence production is an area of weakness for bilingual children with DLD, as it is for monolinguals with DLD. The clinical implications of these findings are discussed.
Accurate and Rapid Forecasts for Geologic Carbon Storage via Learning-Based Inversion-Free Prediction
Authors: Lu Dan , Painter Scott L. , Azzolina Nicholas A. , Burton-Kelly Matthew , Jiang Tao , Williamson Cody
Published: January 2022

Carbon capture and storage (CCS) is one approach being studied by the U.S. Department of Energy to help mitigate global warming. The process involves capturing CO2 emissions from industrial sources and permanently storing them in deep geologic formations (storage reservoirs). However, CCS projects generally target “green field sites,” where there is often little characterization data and therefore large uncertainty about the petrophysical properties and other geologic attributes of the storage reservoir. Consequently, ensemble-based approaches are often used to forecast multiple realizations prior to CO2 injection to visualize a range of potential outcomes. In addition, monitoring data during injection operations are used to update the pre-injection forecasts and thereby improve agreement between forecasted and observed behavior. Thus, a system for generating accurate, timely forecasts of pressure buildup and CO2 movement and distribution within the storage reservoir and for updating those forecasts via monitoring measurements becomes crucial. This study proposes a learning-based prediction method that can accurately and rapidly forecast spatial distribution of CO2 concentration and pressure with uncertainty quantification without relying on traditional inverse modeling. The machine learning techniques include dimension reduction, multivariate data analysis, and Bayesian learning. The outcome is expected to provide CO2 storage site operators with an effective tool for timely and informative decision making based on limited simulation and monitoring data.
A Thermal Chemical Reaction System for Natural Gas Hydrates Exploitation
Authors: Wang Yanan , Sun Zhenxin , Li Qingping , Lv Xin , Ge Yang
Published: January 2022

The methodology of using CO2 to replace CH4 to recover the natural gas hydrates (NGHs) is supposed to avoid geological disasters. However, the reaction path of the CH4–CO2 replacement method is too complex to give satisfactory replacement efficiency. Therefore, this study proposed a thermochemical reaction system that used the heat and the nitrogen released by the thermochemical reactions to recover NGHs. The performance of the thermochemical reaction system (NaNO2 and NH4Cl) regarding heat generation and gas production under low temperature (4°C) conditions was evaluated, and the feasibility of exploiting NGHs with an optimized formula of the thermochemical reaction system was also evaluated in this study. First, the effects of three catalysts (HCl, H₃PO₄, and NH2SO3H) were investigated at the same reactant concentration and catalyst concentration. It was confirmed that HCl as a catalyst can obtain better heat generation and gas production. Second, the effect of HCl concentration on the reaction was investigated under the same reactant concentration. The results showed that the higher the HCl concentration, the faster is the reaction rate. When the concentration of HCl was greater than 14 wt%, side reactions would occur to produce toxic gas; hence, 14 wt% was the optimal catalyst concentration for the reaction of NaNO2 and NH4Cl at low temperatures. Third, the heat generation and gas production of the thermochemical reaction systems were evaluated at different reactant concentrations (1, 2, 3, 4, 5, and 6 mol/L) at 14 wt% HCl concentration. It was found that the best reactant concentration was 5 mol/L. Finally, the feasibility of exploiting NGHs with the optimal system was analyzed from the perspectives of thermal decomposition and nitrogen replacement. The thermochemical reaction system provided by this study is possible to be applied to explore NGHs’ offshore.
Forecasting Scrub Typhus Cases in Eight High-Risk Counties in China: Evaluation of Time-Series Model Performance
Authors: He Junyu , Wei Xianyu , Yin Wenwu , Wang Yong , Qian Quan , Sun Hailong , Xu Yuanyong , Soares Magalhaes Ricardo J. , Guo Yuming , Zhang Wenyi
Published: January 2022

Scrub typhus (ST) is expanding its geographical distribution in China and in many regions worldwide raising significant public health concerns. Accurate ST time-series modeling including uncovering the role of environmental determinants is of great importance to guide disease control purposes. This study evaluated the performance of three competing time-series modeling approaches at forecasting ST cases during 2012–2020 in eight high-risk counties in China. We evaluated the performance of a seasonal autoregressive-integrated moving average (SARIMA) model, a SARIMA model with exogenous variables (SARIMAX), and the long–short term memory (LSTM) model to depict temporal variations in ST cases. In our investigation, we considered eight environmental variables known to be associated with ST landscape epidemiology, including the normalized difference vegetation index (NDVI), temperature, precipitation, atmospheric pressure, sunshine duration, relative humidity, wind speed, and multivariate El Niño/Southern Oscillation index (MEI). The first 8-year data and the last year data were used to fit the models and forecast ST cases, respectively. Our results showed that the inclusion of exogenous variables in the SARIMAX model generally outperformed the SARIMA model. Our results also indicate that the role of exogenous variables with various temporal lags varies between counties, suggesting that ST cases are temporally non-stationary. In conclusion, our study demonstrates that the approach to forecast ST cases needed to take into consideration local conditions in that time-series model performance differed between high-risk areas under investigation. Furthermore, the introduction of time-series models, especially LSTM, has enriched the ability of local public health authorities in ST high-risk areas to anticipate and respond to ST outbreaks, such as setting up an early warning system and forecasting ST precisely.
Emerging Contaminants in Streams of Doce River Watershed, Minas Gerais, Brazil
Authors: Gomes Marcelo Pedrosa , Brito Júlio César Moreira , Vieira Fabio , Kitamura Rafael Shinji Akiyama , Juneau Philippe
Published: January 2022

This study investigated the occurrence and risk assessment of ten pharmaceutical products and two herbicides in the water of rivers from the Doce river watershed (Brazil). Of the 12 chemicals studied, ten (acyclovir, amoxicillin, azithromycin, ciprofloxacin, enrofloxacin, fluoxetine, erythromycin, sulfadiazine, sulfamethoxazole, glyphosate and aminomethylphosphonic acid) had a 100% detection rate. In general, total concentrations of all target drugs ranged from 4.6 to 14.5 μg L−1, with fluoroquinolones and sulfonamides being the most representative classes of pharmaceutical products. Herbicides were found at concentrations at least ten times higher than those of the individual pharmaceutical products and represented the major class of contaminants in the samples. Most of the contaminants studied were above concentrations that pose an ecotoxicological risk to aquatic biota. Urban wastewater must be the main source of contaminants in waterbodies. Our results show that, in addition to the study of metal in water (currently being conducted after the Fundão dam breach), there is an urgent need to monitor emerging contaminant in waters from Doce river watershed rivers, as some chemicals pose environmental risks to aquatic life and humans due to the use of surface water for drinking and domestic purposes by the local population. Special attention should be given to glyphosate, aminomethylphosaphonic acid, and to ciprofloxacin and enrofloxacin (whose concentrations are above predicted levels that induce resistance selection).
Efficiency, Specificity and Temperature Sensitivity of Cas9 and Cas12a RNPs for DNA-free Genome Editing in Plants
Authors: Banakar Raviraj , Schubert Mollie , Kurgan Gavin , Rai Krishan Mohan , Beaudoin Sarah F. , Collingwood Michael A. , Vakulskas Christopher A. , Wang Kan , Zhang Feng
Published: January 2022

Delivery of genome editing reagents using CRISPR-Cas ribonucleoproteins (RNPs) transfection offers several advantages over plasmid DNA-based delivery methods, including reduced off-target editing effects, mitigation of random integration of non-native DNA fragments, independence of vector constructions, and less regulatory restrictions. Compared to the use in animal systems, RNP-mediated genome editing is still at the early development stage in plants. In this study, we established an efficient and simplified protoplast-based genome editing platform for CRISPR-Cas RNP delivery, and then evaluated the efficiency, specificity, and temperature sensitivity of six Cas9 and Cas12a proteins. Our results demonstrated that Cas9 and Cas12a RNP delivery resulted in genome editing frequencies (8.7–41.2%) at various temperature conditions, 22°C, 26°C, and 37°C, with no significant temperature sensitivity. LbCas12a often exhibited the highest activities, while AsCas12a demonstrated higher sequence specificity. The high activities of CRISPR-Cas RNPs at 22° and 26°C, the temperature preferred by plant transformation and tissue culture, led to high mutagenesis efficiencies (34.0–85.2%) in the protoplast-regenerated calli and plants with the heritable mutants recovered in the next generation. This RNP delivery approach was further extended to pennycress (Thlaspi arvense), soybean (Glycine max) and Setaria viridis with up to 70.2% mutagenesis frequency. Together, this study sheds light on the choice of RNP reagents to achieve efficient transgene-free genome editing in plants.
Integrated Dissection of lncRNA-miRNA-mRNA Pairs and Potential Regulatory Role of lncRNA PCAT19 in Lung Adenocarcinoma
Authors: Tang Xiaomei , Hua Xiaoyan , Peng Xujin , Pei Yongyan , Chen Zhigang
Published: January 2022

Lung adenocarcinoma (LUAD) is the main cause of cancer-related deaths worldwide. Long noncoding RNAs have been reported to play an important role in various cancers due to their special functions. Therefore, identifying the lncRNAs involved in LUAD tumorigenesis and development can help improve therapeutic strategies. The TCGA-LUAD RNA expression profile was downloaded from The Cancer Genome Atlas, and a total of 49 differential lncRNAs, 112 differential miRNAs, and 2,953 differential mRNAs were screened. Through Kaplan–Meier curves, interaction networks, hub RNAs (lncRNAs, miRNAs, and mRNAs) were obtained. These hub genes are mainly involved in cell proliferation, cell cycle, lung development, and tumor-related signaling pathways. Two lncRNAs (SMIM25 and PCAT19) more significantly related to the prognosis of LUAD were screened by univariate Cox analysis, multivariate Cox analysis, and risk model analysis. The qPCR results showed that the expression levels of SMIM25 and PCAT19 were downregulated in clinical tissues, A549 and SPC-A1 cells, which were consistent with the bioinformatics analysis results. Subsequently, the PCAT19/miR-143-3p pairs were screened through the weighted gene co-expression network analysis and miRNA-lncRNA regulatory network. Dual luciferase detection confirmed that miR-143-3p directly targets PCAT19, and qPCR results indicated that the expression of the two is positively correlated. Cell function tests showed that overexpression of PCAT19 could significantly inhibit the proliferation, migration, and invasion of A549 and SPC-A1 cells. In contrast, knockout of PCAT19 can better promote the proliferation and migration of A549 and SPC-A1 cells. The expression of PCAT19 was negatively correlated with tumor grade, histological grade, and tumor mutation load in LUAD. In addition, co-transfection experiments confirmed that the miR-143-3p mimic could partially reverse the effect of PCAT19 knockout on the proliferation of A549 and SPC-A1 cells. In summary, PCAT19 is an independent prognostic factor in patients with LUAD that can regulate the proliferation, migration, and invasion of LUAD cells and may be a potential biomarker for the diagnosis of LUAD. PCAT19/miR-143-3p plays a very important regulatory role in the occurrence and development of LUAD.
Gene-Environment Interaction Analysis Incorporating Sex, Cardiometabolic Diseases, and Multiple Deprivation Index Reveals Novel Genetic Associations With COVID-19 Severity
Authors: Westerman Kenneth E. , Lin Joanna , Sevilla-Gonzalez Magdalena del Rocio , Tadess Beza , Marchek Casey , Manning Alisa K.
Published: January 2022

Increasing evidence indicates that specific genetic variants influence the severity of outcomes after infection with COVID-19. However, it is not clear whether the effect of these genetic factors is independent of the risk due to more established non-genetic demographic and metabolic risk factors such as male sex, poor cardiometabolic health, and low socioeconomic status. We sought to identify interactions between genetic variants and non-genetic risk factors influencing COVID-19 severity via a genome-wide interaction study in the UK Biobank. Of 378,051 unrelated individuals of European ancestry, 2,402 were classified as having experienced severe COVID-19, defined as hospitalization or death due to COVID-19. Exposures included sex, cardiometabolic risk factors [obesity and type 2 diabetes (T2D), tested jointly], and multiple deprivation index. Multiplicative interaction was tested using a logistic regression model, conducting both an interaction test and a joint test of genetic main and interaction effects. Five independent variants reached genome-wide significance in the joint test, one of which also reached significance in the interaction test. One of these, rs2268616 in the placental growth factor (PGF) gene, showed stronger effects in males and in individuals with T2D. None of the five variants showed effects on a similarly-defined phenotype in a lookup in the COVID-19 Host Genetics Initiative. These results reveal potential additional genetic loci contributing to COVID-19 severity and demonstrate the value of including non-genetic risk factors in an interaction testing approach for genetic discovery.
CD209/CD14+ Dendritic Cells Characterization in Rheumatoid and Psoriatic Arthritis Patients: Activation, Synovial Infiltration, and Therapeutic Targeting
Authors: Marzaioli Viviana , Canavan Mary , Floudas Achilleas , Flynn Keelin , Mullan Ronan , Veale Douglas J. , Fearon Ursula
Published: January 2022

Dendritic cells (DC) have a key role in the initiation and progression of inflammatory arthritis (IA). In this study, we identified a DC population that derive from monocytes, characterized as CD209/CD14+ DC, expressing classical DC markers (HLADR, CD11c) and the Mo-DC marker (CD209), while also retaining the monocytic marker CD14. This CD209/CD14+ DC population is present in the circulation of Healthy Control (HC), with increased frequency in Rheumatoid Arthritis (RA) and Psoriatic arthritic (PsA) patients. We demonstrate, for the first time, that circulatory IA CD209/CD14+ DC express more cytokines (IL1β/IL6/IL12/TNFα) and display a unique chemokine receptor expression and co-expression profiles compared to HC. We demonstrated that CD209/CD14+ DC are enriched in the inflamed joint where they display a unique inflammatory and maturation phenotype, with increased CD40 and CD80 and co-expression of specific chemokine receptors, displaying unique patterns between PsA and RA. We developed a new protocol of magnetic isolation and expansion for CD209+ DC from blood and identified transcriptional differences involved in endocytosis/antigen presentation between RA and PsA CD209+ DC. In addition, we observed that culture of healthy CD209+ DC with IA synovial fluid (SF), but not Osteoarthritis (OA) SF, was sufficient to induce the development of CD209/CD14+ DC, leading to a poly-mature DC phenotype. In addition, differential effects were observed in terms of chemokine receptor and chemokine expression, with healthy CD209+ DC displaying increased expression/co-expression of CCR6, CCR7, CXCR3, CXCR4 and CXCR5 when cultured with RA SF, while an increase in the chemokines CCR3, CXCL10 and CXCL11 was observed when cultured with PsA SF. This effect may be mediated in part by the observed differential increase in chemokines expressed in RA vs PsA SF. Finally, we observed that the JAK/STAT pathway, but not the NF-κB pathway (driven by TNFα), regulated CD209/CD14+ DC function in terms of activation, inflammatory state, and migratory capacity. In conclusion, we identified a novel CD209/CD14+ DC population, which is active in the circulation of RA and PsA, an effect potentiated once they enter the joint. Furthermore, we demonstrated that JAK/STAT inhibition can be used as a therapeutic strategy to decrease the inflammatory state of the pathogenic CD209/CD14+ DC.
Analysis of T-Cell Receptor Repertoire in Transplantation: Fingerprint of T Cell-mediated Alloresponse
Authors: Tian Guangyao , Li Mingqian , Lv Guoyue
Published: January 2022

T cells play a key role in determining allograft function by mediating allogeneic immune responses to cause rejection, and recent work pointed their role in mediating tolerance in transplantation. The unique T-cell receptor (TCR) expressed on the surface of each T cell determines the antigen specificity of the cell and can be the specific fingerprint for identifying and monitoring. Next-generation sequencing (NGS) techniques provide powerful tools for deep and high-throughput TCR profiling, and facilitate to depict the entire T cell repertoire profile and trace antigen-specific T cells in circulation and local tissues. Tailing T cell transcriptomes and TCR sequences at the single cell level provides a full landscape of alloreactive T-cell clones development and biofunction in alloresponse. Here, we review the recent advances in TCR sequencing techniques and computational tools, as well as the recent discovery in overall TCR profile and antigen-specific T cells tracking in transplantation. We further discuss the challenges and potential of using TCR sequencing-based assays to profile alloreactive TCR repertoire as the fingerprint for immune monitoring and prediction of rejection and tolerance.
Increased Circulating Cell-Free DNA in Eosinophilic Granulomatosis With Polyangiitis: Implications for Eosinophil Extracellular Traps and Immunothrombosis
Authors: Hashimoto Teppei , Ueki Shigeharu , Kamide Yosuke , Miyabe Yui , Fukuchi Mineyo , Yokoyama Yuichi , Furukawa Tetsuya , Azuma Naoto , Oka Nobuyuki , Takeuchi Hiroki , Kanno Kyoko , Ishida-Yamamoto Akemi , Taniguchi Masami , Hashiramoto Akira , Matsui Kiyoshi
Published: January 2022

Background

Endogenous DNA derived from nuclei or mitochondria is released into the blood circulation as cell-free DNA (cfDNA) following cell damage or death. cfDNA is associated with various pathological conditions; however, its clinical significance in antineutrophil cytoplasmic antibody-associated vasculitis (AAV) remains unclear. This study aimed to evaluate the clinical significance of cfDNA in AAV.

Methods

We enrolled 35 patients with AAV, including 10 with eosinophilic granulomatosis with polyangiitis (EGPA), 13 with microscopic polyangiitis, and 12 with granulomatosis with polyangiitis. Serum cf-nuclear DNA (cf-nDNA) and cf-mitochondrial DNA (cf-mtDNA) levels were measured by quantitative polymerase chain reaction before and after the initiation of immunosuppressive therapy. Tissue samples from EGPA patients were examined by immunofluorescence and transmission electron microscopy. The structure of eosinophil extracellular traps (EETs) and neutrophil extracellular traps (NETs) and stability against DNase were assessed in vitro. Platelet adhesion of EETs were also assessed.

Results

Serum cf-nDNA and cf-mtDNA levels were significantly higher in AAV than in healthy controls, with the highest levels in EGPA; however, serum DNase activities were comparable among all groups. cf-nDNA and cf-mtDNA decreased after treatment and were associated with disease activity only in EGPA. Blood eosinophil count and plasma D-dimer levels were significantly correlated with cf-nDNA in EGPA and cf-mtDNA. EGPA tissue samples showed lytic eosinophils and EETs in small-vessel thrombi. The structure of EETs showed bolder net-like chromatin threads in vitro and EETs showed greater stability against DNase than NETs. EETs provided a scaffold for platelet adhesion.

Conclusion

cfDNA was increased in EGPA, associated with disease activity. The presence of DNase-resistant EETs in small-vessel thrombi might contribute to higher concentration of cfDNA and the occurrence of immunothrombosis in EGPA.
An Overview of Transcriptional Responses of Schistosome-Susceptible (M line) or -Resistant (BS-90) Biomphalaria glabrata Exposed or Not to Schistosoma mansoni Infection
Authors: Lu Lijun , Bu Lijing , Zhang Si-Ming , Buddenborg Sarah K. , Loker Eric S.
Published: January 2022

Background

We seek to provide a comprehensive overview of transcriptomics responses of immune-related features of the gastropod Biomphalaria glabrata (Bg) following exposure to Schistosoma mansoni (Sm), a trematode causing human schistosomiasis. Responses of schistosome-susceptible (M line, or SUS) and -resistant (BS-90, or RES) Bg strains were characterized following exposure to Sm for 0.5, 2, 8 or 40 days post-exposure (dpe).

Methods

RNA-Seq and differential expression analysis were undertaken on 56 snails from 14 groups. We considered 7 response categories: 1) constitutive resistance factors; 2) constitutive susceptibility factors; 3) generalized stress responses; 4) induced resistance factors; 5) resistance factors suppressed in SUS snails; 6) suppressed/manipulated factors in SUS snails; and 7) tolerance responses in SUS snails. We also undertook a gene co-expression network analysis. Results from prior studies identifying schistosome resistance/susceptibility factors were examined relative to our findings.

Results

A total of 792 million paired-end reads representing 91.2% of the estimated 31,985 genes in the Bg genome were detected and results for the 7 categories compiled and highlighted. For both RES and SUS snails, a single most supported network of genes with highly correlated expression was found.

Conclusions

1) Several constitutive differences in gene expression between SUS and RES snails were noted, the majority over-represented in RES; 2) There was little indication of a generalized stress response shared by SUS and RES snails at 0.5 or 2 dpe; 3) RES snails mounted a strong, multi-faceted response by 0.5 dpe that carried over to 2 dpe; 4) The most notable SUS responses were at 40 dpe, in snails shedding cercariae, when numerous features were either strongly down-regulated indicative of physiological distress or parasite manipulation, or up-regulated, suggestive of tolerance or survival-promoting effects; 5) Of 55 genes previously identified in genome wide mapping studies, 29 (52.7%) were responsive to Sm, as were many familiar resistance-associated genes (41.0%) identified by other means; 6) Both network analysis and remarkably specific patterns of expression of lectins and G protein-coupled receptors in categories 4, 6 and 7 were indicative of orchestrated responses of different suites of genes in SUS or RES snails following exposure to Sm.
Mesenchymal Stem Cells Derived Extracellular Vesicles Alleviate Traumatic Hemorrhagic Shock Induced Hepatic Injury via IL-10/PTPN22-Mediated M2 Kupffer Cell Polarization
Authors: Zhang Yunwei , Zhang Xiaofei , Zhang Hongji , Song Peng , Pan Wenming , Xu Peng , Wang Guoliang , Hu Ping , Wang Zixuan , Huang Kunpeng , Zhang Xiaodong , Wang Hui , Zhang Jinxiang
Published: January 2022

Traumatic hemorrhagic shock (THS) is a major cause of mortality and morbidity worldwide in severely injured patients. Mesenchymal stem cells (MSCs) possess immunomodulatory properties and tissue repair potential mainly through a paracrine pathway mediated by MSC-derived extracellular vesicles (MSC-EVs). Interleukin 10 (IL-10) is a potent anti-inflammatory cytokine that plays a crucial role during the inflammatory response, with a broad range of effects on innate and adaptive immunity, preventing damage to the host and maintaining normal tissue homeostasis. However, the function and mechanism of IL-10 in MSC-mediated protective effect in THS remain obscure. Here, we show that MSCs significantly attenuate hepatic injury and inflammation from THS in mice. Notably, these beneficial effects of MSCs disappeared when IL-10 was knocked out in EVs or when recombinant IL-10 was administered to mice. Mechanistically, MSC-EVs function to carry and deliver IL-10 as cargo. WT MSC-EVs restored the function of IL-10 KO MSCs during THS injury. We further demonstrated that EVs containing IL-10 mainly accumulated in the liver during THS, where they were captured by Kupffer cells and induced the expression of PTPN22. These effects subsequently shifted Kupffer cells to an anti-inflammatory phenotype and mitigated liver inflammation and injury. Therefore, our study indicates that MSC-EVs containing IL-10 alleviate THS-induced hepatic injury and may serve as a cell-free therapeutic approach for THS.
Good’s Syndrome: Time to Move on From Reviewing the Past
Authors: Kabir Aunonna , Alizadehfar Reza , Tsoukas Christos M.
Published: January 2022

For seven decades, the pathophysiology of Good’s syndrome (GS) has remained a mystery, with few attempts to solve it. Initially described as an association between hypogammaglobulinemia and thymoma, controversy exists whether this is a unique disease, or a subgroup of Common Variable Immune Deficiency (CVID). Recently, some distinguishing aspects of both syndromes have come to light reflecting fundamental differences in their underlying pathophysiology. GS and CVID differ in demographic features and immune phenotype. GS is found almost exclusively in adults and is characterized by a significantly reduced or absence of peripheral B cells. In CVID, which also occurs in children, most patients have normal or slightly reduced peripheral B cells, with a distinguishing feature of low memory B cells. Similarly, differences in T cell dysregulation and manifestations of hematologic cytopenias may further distinguish GS from CVID. Knowledge of the clinical phenotype of this rare adult immune deficiency stems from individual case reports, retrospective, and cross-sectional data on a few cohorts with a limited number of well characterized patients. The understanding of pathophysiology in GS is hampered by the incomplete and inconsistent reporting of clinical and laboratory data, with a limited knowledge of its natural history. In this mini review, we discuss current state of the art data and identify research gaps. In order to resolve controversies and fill in knowledge gaps, we propose a coordinated paradigm shift from incidence reporting to robust investigative studies, addressing mechanisms of disease. We hope this novel approach sets a clear direction to solve the current controversies.
Artificial Upwelling in Singular and Recurring Mode: Consequences for Net Community Production and Metabolic Balance
Authors: Ortiz Joaquin , Arístegui Javier , Taucher Jan , Riebesell Ulf
Published: January 2022

Artificial upwelling of nutrient-rich waters and the corresponding boost in primary productivity harbor the potential to enhance marine fishery yields and strengthen the biological pump for sequestration of atmospheric CO2. There is increasing urgency to understand this technology as a “ocean-based solution” for counteracting two major challenges of the 21st century—climate change and overfishing. Yet, little is known about the actual efficacy and/or possible side effects of artificial upwelling. We conducted a large-scale off-shore mesocosm study (∼44 m3) in the oligotrophic waters of the Canary Islands to identify the community-level effects of artificial upwelling on a natural oligotrophic plankton community. Four upwelling intensities were simulated (approx. 1.5/3/5.7/10 μmol L–1 of nitrate plus phosphate and silicate) via two different upwelling modes (a singular deep-water pulse vs. recurring supply every 4 days) for 37 days. Here we present results on the response of net community production (NCP), metabolic balance and phytoplankton community composition (<250 μm). Higher upwelling intensities yielded higher cumulative NCP. Following upwelling onset, the phytoplankton community became dominated by diatoms in all treatments, but other taxa such as Coccolithophores increased later in the experiment. The magnitude of effects on the metabolic balance scaled with the amount of added deep water, leading to (i) a balanced to net-heterotrophic system in the singular and (ii) a net-autotrophic system in the recurring upwelling treatments. Accordingly, the mode in which nutrients are supplied to an oligotrophic system plays a crucial role in the ecosystem response, with recurring upwelling leading to higher long-term positive NCP than singular upwelling. These results highlight the importance of empirically measured local responses to upwelling such as community structure and metabolism, with major implications for the potential employment of artificial upwelling as an ocean-based solution to generate (primary) production.
Prototype-Scale Physical Model of Wave Attenuation Through a Mangrove Forest of Moderate Cross-Shore Thickness: LiDAR-Based Characterization and Reynolds Scaling for Engineering With Nature
Authors: Kelty Kiernan , Tomiczek Tori , Cox Daniel Thomas , Lomonaco Pedro , Mitchell William
Published: January 2022

This study investigates the potential of a Rhizophora mangrove forest of moderate cross-shore thickness to attenuate wave heights using an idealized prototype-scale physical model constructed in a 104 m long wave flume. An 18 m long cross-shore transect of an idealized red mangrove forest based on the trunk-prop root system was constructed in the flume. Two cases with forest densities of 0.75 and 0.375 stems/m2 and a third baseline case with no mangroves were considered. LiDAR was used to quantify the projected area per unit height and to estimate the effective diameter of the system. The methodology was accurate to within 2% of the known stem diameters and 10% of the known prop root diameters. Random and regular wave conditions seaward, throughout, and inland of the forest were measured to determine wave height decay rates and drag coefficients for relative water depths ranging 0.36 to 1.44. Wave height decay rates ranged 0.008–0.021 m–1 for the high-density cases and 0.004–0.010 m–1 for the low-density cases and were found to be a function of water depth. Doubling the forest density increased the decay rate by a factor two, consistent with previous studies for other types of emergent vegetation. Drag coefficients ranged 0.4–3.8, and were found to be dependent on the Reynolds number. Uncertainty in the estimates of the drag coefficient due to the measured projected area and measured wave attenuation was quantified and found to have average combined standard deviations of 0.58 and 0.56 for random and regular waves, respectively. Two previous reduced-scale studies of wave attenuation by mangroves compared well with the present study when their Reynolds numbers were re-scaled by λ3/2 where λ is the prototype-to-model geometric scale ratio. Using the combined data sets, an equation is proposed to estimate the drag coefficient for a Rhizophora mangrove forest: CD = 0.6 + 3e04/ReDBH with an uncertainty of 0.69 over the range 5e03 < ReDBH < 1.9e05, where ReDBH is based on the tree diameter at breast height. These results may improve engineering guidance for the use of mangroves and other emergent vegetation in coastal wave attenuation.