bluuebunny/crossref_metadata_2025_split huggingface dataset:
SIV infection and ARV treatment reshape the transcriptional and epigenetic profile of naïve and memory T cells
in vivo
Authors: Rahmberg Andrew R. , Markowitz Tovah E. , Mudd Joseph C. , Ortiz Alexandra M. , Brenchley Jason M. 
Published: May 2024

ABSTRACT

Human and simian immunodeficiency viruses (HIV and SIV) are lentiviruses that reverse transcribe their RNA genome with subsequent integration into the genome of the target cell. How progressive infection and administration of antiretrovirals (ARVs) longitudinally influence the transcriptomic and epigenetic landscape of particular T cell subsets, and how these may influence the genetic location of integration are unclear. Here, we use RNAseq and ATACseq to study the transcriptomics and epigenetic landscape of longitudinally sampled naïve and memory CD4+ and CD8+ T cells in two species of non-human primates prior to SIV infection, during chronic SIV infection, and after administration of ARVs. We find that SIV infection leads to significant alteration to the transcriptomic profile of all T cell subsets that are only partially reversed by administration of ARVs. Epigenetic changes were more apparent in animals with longer periods of untreated SIV infection and correlated well with changes in corresponding gene expression. Known SIV integration sites did not vary due to SIV status but did contain more open chromatin in rhesus macaque memory T cells, and the expression of proteasome-related genes at the pre-SIV timepoint correlated with subsequent viremia.

IMPORTANCE
Chronic inflammation during progressive human and simian immunodeficiency virus (HIV and SIV) infections leads to significant co-morbidities in infected individuals with significant consequences. Antiretroviral (ARV)-treated individuals also manifest increased levels of inflammation which are associated with increased mortalities. These data will help guide rational development of modalities to reduce inflammation observed in people living with HIV and suggest mechanisms underlying lentiviral integration site preferences.
Transmissible gastroenteritis virus induces inflammatory responses via RIG-I/NF-κB/HIF-1α/glycolysis axis in intestinal organoids and
in vivo
Authors: Zhang Yunhang , Yang Ning , Li Yang , Tan Chen , Cai Yifei , Rui Xue , Liu Yuanyuan , Fu Yuguang , Liu Guangliang 
Published: May 2024

ABSTRACT

Transmissible gastroenteritis virus (TGEV)-induced enteritis is characterized by watery diarrhea, vomiting, and dehydration, and has high mortality in newborn piglets, resulting in significant economic losses in the pig industry worldwide. Conventional cell lines have been used for many years to investigate inflammation induced by TGEV, but these cell lines may not mimic the actual intestinal environment, making it difficult to obtain accurate results. In this study, apical-out porcine intestinal organoids were employed to study TEGV-induced inflammation. We found that apical-out organoids were susceptible to TGEV infection, and the expression of representative inflammatory cytokines was significantly upregulated upon TGEV infection. In addition, retinoic acid-inducible gene I (RIG-I) and the nuclear factor-kappa B (NF-κB) pathway were responsible for the expression of inflammatory cytokines induced by TGEV infection. We also discovered that the transcription factor hypoxia-inducible factor-1α (HIF-1α) positively regulated TGEV-induced inflammation by activating glycolysis in apical-out organoids, and pig experiments identified the same molecular mechanism as the
ex vivo
results. Collectively, we unveiled that the inflammatory responses induced by TGEV were modulated via the RIG-I/NF-κB/HIF-1α/glycolysis axis
ex vivo
and
in vivo
. This study provides novel insights into TGEV-induced enteritis and verifies intestinal organoids as a reliable model for investigating virus-induced inflammation.

IMPORTANCE
Intestinal organoids are a newly developed culture system for investigating immune responses to virus infection. This culture model better represents the physiological environment compared with well-established cell lines. In this study, we discovered that inflammatory responses induced by TGEV infection were regulated by the RIG-I/NF-κB/HIF-1α/glycolysis axis in apical-out porcine organoids and in pigs. Our findings contribute to understanding the mechanism of intestinal inflammation upon viral infection and highlight apical-out organoids as a physiological model to mimic virus-induced inflammation.
Tripartite motif-containing protein 21 is involved in IFN-γ-induced suppression of hepatitis B virus by regulating hepatocyte nuclear factors
Authors: Won Juhee , Kang Hong Seok , Kim Na Yeon , Dezhbord Mehrangiz , Marakkalage Kamindu Gayashan , Lee Eun-Hwi , Lee Donghyo , Park Soree , Kim Dong-Sik , Kim Kyun-Hwan 
Published: May 2024

ABSTRACT

The antiviral role of the tripartite motif-containing (TRIM) protein family , a member of the E3-ubiquitin ligase family, has recently been actively studied. Hepatitis B virus (HBV) infection is a major contributor to liver diseases; however, the host factors regulated by cytokine-inducible TRIM21 to suppress HBV remain unclear. In this study, we showed the antiviral efficacy of TRIM21 against HBV in hepatoma cell lines, primary human hepatocytes isolated from patient liver tissues, and mouse model. Using TRIM21 knock-out cells, we confirmed that the antiviral effects of interferon-gamma, which suppress HBV replication, are diminished when TRIM21 is deficient. Northern blot analysis confirmed a reduction of HBV RNA levels by TRIM21. Using Luciferase reporter assay, we also discovered that TRIM21 decreases the activity of HBV enhancers, which play a crucial role in covalently closed circular DNA transcription. The participation of the RING domain and PRY-SPRY domain in the anti-HBV effect of TRIM21 was demonstrated through experiments using deletion mutants. We identified a novel interaction between TRIM21 and hepatocyte nuclear factor 4α (HNF4α) through co-immunoprecipitation assay. More specifically, ubiquitination assay revealed that TRIM21 promotes ubiquitin-mediated proteasomal degradation of HNF4α. HNF1α transcription is down-regulated as a result of the degradation of HNF4α, an activator for the HNF1α promoter. Therefore, the reduction of key HBV enhancer activators, HNF4α and HNF1α, by TRIM21 resulted in a decline in HBV transcription, ultimately leading to the inhibition of HBV replication.

IMPORTANCE
Despite extensive research efforts, a definitive cure for chronic hepatitis B remains elusive, emphasizing the persistent importance of this viral infection as a substantial public health concern. Although the risks associated with hepatitis B virus (HBV) infection are well known, host factors capable of suppressing HBV are largely uncharacterized. This study elucidates that tripartite motif-containing protein 21 (TRIM21) suppresses HBV transcription and consequently inhibits HBV replication by downregulating the hepatocyte nuclear factors, which are host factors associated with the HBV enhancers. Our findings demonstrate a novel anti-HBV mechanism of TRIM21 in interferon-gamma-induced anti-HBV activity. These findings may contribute to new strategies to block HBV.
Aberrant RNA polymerase initiation and processivity on the genome of a herpes simplex virus 1 mutant lacking ICP27
Authors: Birkenheuer Claire H. , Baines Joel D. 
Published: May 2024

ABSTRACT

Within the first 15 minutes of infection, herpes simplex virus 1 immediate early proteins repurpose cellular RNA polymerase (Pol II) for viral transcription. An important role of the viral-infected cell protein 27 (ICP27) is to facilitate viral pre-mRNA processing and export viral mRNA to the cytoplasm. Here, we use precision nuclear run-on followed by deep sequencing (PRO-seq) to characterize transcription of a viral ICP27 null mutant. At 1.5 and 3 hours post infection (hpi), we observed increased total levels of Pol II on the mutant viral genome and accumulation of Pol II downstream of poly A sites indicating increased levels of initiation and processivity. By 6 hpi, Pol II accumulation on specific mutant viral genes was higher than that on wild-type virus either at or upstream of poly A signals, depending on the gene. The PRO-seq profile of the ICP27 mutant on late genes at 6 hpi was similar but not identical to that caused by treatment with flavopiridol, a known inhibitor of RNA processivity. This pattern was different from PRO-seq profiles of other
α
gene mutants and upon inhibition of viral DNA replication with PAA. Together, these results indicate that ICP27 contributes to the repression of aberrant viral transcription at 1.5 and 3 hpi by inhibiting initiation and decreasing RNA processivity. However, ICP27 is needed to enhance processivity on most late genes by 6 hpi in a mechanism distinguishable from its role in viral DNA replication.

IMPORTANCE
We developed and validated the use of a processivity index for precision nuclear run-on followed by deep sequencing data. The processivity index calculations confirm infected cell protein 27 (ICP27) induces downstream of transcription termination on certain host genes. The processivity indices and whole gene probe data implicate ICP27 in transient immediate early gene-mediated repression, a process that also requires ICP4, ICP22, and ICP0. The data indicate that ICP27 directly or indirectly regulates RNA polymerase (Pol II) initiation and processivity on specific genes at specific times post infection. These observations support specific and varied roles for ICP27 in regulating Pol II activity on viral genes in addition to its known roles in post transcriptional mRNA processing and export.
Improved protein splicing through viral passaging
Authors: Hume Adam J. , Deeney Dylan J. , Smetana John S. , Turcinovic Jacquelyn , Connor John H. , Belfort Marlene , Mühlberger Elke , Lennon Christopher W. 
Published: May 2024

ABSTRACT

In
tervening pro
teins
(inteins) are translated as subdomains within host proteins and removed through an intein-driven splicing reaction where the flanking sequences (exteins) are joined with a peptide bond. Previously, we developed a self-removing translation reporter for labeling Ebola virus (EBOV). In this reporter, an intein (RadA) containing the fluorescent protein ZsGreen (ZsG) is inserted within the EBOV protein VP30. Upon VP30-RadA-ZsG expression from the viral genome, RadA-ZsG is removed from VP30 through the protein splicing activity of RadA, generating functional, non-tagged VP30 and functional ZsGreen. While incorporation of our VP30-RadA-ZsG fusion reporter into recombinant EBOV (rEBOV-RadA-ZsG) resulted in an infectious virus that expresses ZsG upon infection of cells, this virus displayed a replication defect compared to wild-type EBOV, which might be the result of insufficient RadA splicing. Here, we demonstrate that the serial passaging of rEBOV-RadA-ZsG in human cells led to an increase in replication efficiency compared to unpassaged rEBOV-RadA-ZsG. Sequencing of passaged viruses revealed intein-specific mutations. These mutations improve intein activity in both prokaryotic and eukaryotic systems, as well as in multiple extein contexts. Taken together, our findings offer a novel means to select for inteins with enhanced catalytic properties that appear independent of extein context and expression system.

IMPORTANCE

In
tervening pro
teins
(inteins) are self-removing protein elements that have been utilized to develop a variety of innovative protein engineering technologies. Here, we report the isolation of inteins with improved catalytic activity through viral passaging. Specifically, we inserted a highly active intein within an essential protein of Ebola virus and serially passaged this recombinant virus, which led to intein-specific hyper-activity mutations. The identified mutations showed improved intein activity within both bacterial and eukaryotic expression systems and in multiple extein contexts. These results present a new strategy for developing inteins with improved splicing activity.
From evidence to tailored decision-making: a qualitative research of barriers and facilitating factors for the implementation of non-clinical interventions to reduce unnecessary caesarean section in Romania
Authors: Berdzuli Nino , Llop-Gironés Alba , Farcasanu Dana , Butu Cassandra , Grbic Miljana , Betran Ana Pilar 
Published: May 2024

ObjectiveTo improve understanding of the drivers of the increased caesarean section (CS) rate in Romania and to identify interventions to reverse this trend, as well as barriers and facilitators.DesignA formative research study was conducted in Romania between November 2019 and February 2020 by means of in-depth interviews and focus-group discussions. Romanian decision-makers and high-level obstetricians preselected seven non-clinical interventions for consideration. Thematic content analysis was carried out.Participants88 women and 26 healthcare providers and administrators.SettingsCounties with higher and lower CS rates were selected for this research—namely Argeș, Bistrița-Năsăud, Brașov, Ialomița, Iași, Ilfov, Dolj and the capital city of București (Bucharest).ResultsWomen wanted information, education and support. Obstetricians feared malpractice lawsuits; this was identified as a key reason for performing CSs. Most obstetrics and gynaecology physicians would oppose policies of mandatory second opinions, financial measures to equalise payments for vaginal and CS births and goal setting for CS rates. In-service training was identified as a need by obstetricians, midwives and nurses. In addition, relevant structural constraints were identified: perceived lower quality of care for vaginal birth, a lack of obstetricians with expertise in managing complicated vaginal births, a lack of anaesthesiologists and midwives, and family doctors not providing antenatal care. Finally, women expressed the need to ensure their rights to dignified and respectful healthcare through pregnancy and childbirth.ConclusionConsideration of the views, values and preferences of all stakeholders in a multifaceted action tailored to Romanian determinants is critical to address relevant determinants to reduce unnecessary CSs. Further studies should assess the effect of multifaceted interventions.
Aspirin versus metformin in pregnancies at high risk of preterm pre-eclampsia in China (AVERT): protocol for a multicentre, double-blind, 3-arm randomised controlled trial
Authors: Liu Jiao , Shen Lixia , Nguyen-Hoang Long , Zhou Qiongjie , Wang Chi Chiu , Lu Xiaohong , Sahota Daljit , Chong Ka Chun , Ying Hao , Gu Weirong , Zhou Rong , Yang Huixia , Jiang Yanmin , Chen Dunjin , Li Xiaotian , Poon Liona 
Published: May 2024

Introduction
Pre-eclampsia (PE) affects about 5% of Chinese pregnant women and is a major cause of maternal and perinatal morbidity and mortality. The first trimester screening model developed by the Fetal Medicine Foundation, which uses the Bayes theorem to combine maternal characteristics and medical history together with measurements of biomarkers, has been proven to be effective and has superior screening performance to that of the traditional risk factor-based approach for the prediction of PE. Prophylactic use of low-dose aspirin in women at risk for PE has resulted in a lower incidence of preterm-PE. However, there is no consensus on the preferred aspirin dosage for the prevention of preterm-PE. Evidence has also suggested that metformin has the potential benefit in preventing PE in pregnant women who are at high risk of the disorder.

Method and analysis
We present a protocol (V.2.0, date 17 March 2022) for the AVERT trial, which is a multicentre, double-blinded, 3-arm randomised controlled trial (RCT) that uses an effective PE screening programme to explore the optimal dosage of aspirin and the role of metformin for the prevention of PE among high-risk pregnant women in China. We intend to recruit 66 000 singleton pregnancies without treatment of low-dose aspirin and metformin at 11–13 weeks’ gestation and all eligible women attending for their first trimester routine scan will be invited to undergo screening for preterm-PE by the combination of maternal factors, mean arterial pressure and placental growth factor. Women found to be at high risk of developing preterm-PE will be invited to take part in the RCT. This study will compare the incidence of preterm-PE with delivery at <37 weeks’ gestation, as the primary outcome, of three different interventional groups: (1) aspirin 75 mg daily, (2) aspirin 150 mg daily and (3) aspirin 75 mg with metformin 1.5 g daily. 957 participants per treatment group are required to detect a significant difference of 59% in the reduction of the incidence of preterm-PE with 80% power and type I error of 5%. Pregnancy and neonatal outcomes will be collected and analysed.

Ethics and dissemination
Ethical approval for the study was obtained from the Joint Chinese University of Hong Kong–New Territories East Cluster Clinical Research Ethics Committee (CREC Ref. No. 2021.406) in Hong Kong and the Ethics Committee of each participating hospital in Mainland China. The study is registered at ClinicalTrials.gov. The results of the AVERT trial will be disseminated at international academic conferences and published in high-impact factor journals.

Trial registration number

NCT05580523
.
Multicentre, randomised, double-blind, placebo-controlled, proof of concept study of LSALT peptide as prevention of acute respiratory distress syndrome and acute kidney injury in patients infected with SARS-CoV-2 (COVID-19)
Authors: Somayaji Ranjani , Luke David R , Lau Arthur , Guner Rahmet , Tabak Ŏ Fehmi , Hepokoski Mark , Gardetto Nancy , Conrad Steven A , Kumar Sunil D , Ghosh Kalyan , Robbins Stephen M , Senger Donna L , Sun Daisy , Lim Rachel K S , Liu Jonathan , Eser Fatma , Karaali Ridvan , Tremblay Alain , Muruve Daniel 
Published: May 2024

ObjectiveDipeptidase-1 (DPEP-1) is a recently discovered leucocyte adhesion receptor for neutrophils and monocytes in the lungs and kidneys and serves as a potential therapeutic target to attenuate inflammation in moderate-to-severe COVID-19. We aimed to evaluate the safety and efficacy of the DPEP-1 inhibitor, LSALT peptide, to prevent specific organ dysfunction in patients hospitalised with COVID-19.DesignPhase 2a randomised, placebo-controlled, double-blinded, trial.SettingHospitals in Canada, Turkey and the USA.ParticipantsA total of 61 subjects with moderate-to-severe COVID-19.InterventionsRandomisation to LSALT peptide 5 mg intravenously daily or placebo for up to 14 days.Primary and secondary outcome measuresThe primary endpoint was the proportion of subjects alive and free of respiratory failure and/or the need for renal replacement therapy (RRT). Numerous secondary and exploratory endpoints were assessed including ventilation-free days, and changes in kidney function or serum biomarkers.ResultsAt 28 days, 27 (90.3%) and 28 (93.3%) of subjects in the placebo and LSALT groups were free of respiratory failure and the need for RRT (p=0.86). On days 14 and 28, the number of patients still requiring more intensive respiratory support (O2≥6 L/minute, non-invasive or invasive mechanical ventilation or extracorporeal membrane oxygenation) was 6 (19.4%) and 3 (9.7%) in the placebo group versus 2 (6.7%) and 2 (6.7%) in the LSALT group, respectively (p=0.14; p=0.67). Unadjusted analysis of ventilation-free days demonstrated 22.8 days for the LSALT group compared with 20.9 in the placebo group (p=0.4). LSALT-treated subjects had a significant reduction in the fold expression from baseline to end of treatment of serum CXCL10 compared with placebo (p=0.02). Treatment-emergent adverse events were similar between groups.ConclusionIn a Phase 2 study, LSALT peptide was demonstrated to be safe and tolerated in patients hospitalised with moderate-to-severe COVID-19.Trial registration numberNCT04402957.
Characteristics of patients who seek medical attention for headache and those who do not: cross-sectional survey and linked medical claims data analysis in Japan
Authors: Igarashi Hisaka , Sano Hiromi , Kondo Hiroyuki , Shibasaki Yoshiyuki , Koga Nobuyuki 
Published: May 2024

ObjectiveTo describe the characteristics of patients who sought medical attention for headache and those who did not.DesignThis observational study used a cross-sectional online survey and linked medical claims data.SettingData from an online self-administered questionnaire survey conducted in November 2020 as well as linked medical claims data spanning December 2017 and November 2020 were provided by DeSC Healthcare Inc.ParticipantsOf 21 480 respondents aged 19–74 years whose sex and age data matched the claims data, 7311 reported experiencing headache.MeasuresOutcomes included participant characteristics, status of medical attention seeking, medication use, quality of life (QOL) measured by Migraine-Specific QOL (MSQ) questionnaire V.2.1 and headache intensity.ResultsOf the 7311 respondents with headache, 735 sought medical attention and 6576 did not. Compared with those who did not seek medical attention, those who sought medical attention had more frequent headaches (median: 5 days/3 months vs 10 days/3 months in those who did not vs those who sought medical attention, respectively) had lower MSQ score (mean (SD) MSQ total score: 87.6 (13.0) vs 77.1 (18.1)) and were likely to experience moderately severe to severe headache (19.0% (1252/6576) vs 41.2% (303/735)) without headache medication. The inability to tolerate headache (36.5% (268/735)) was a common reason for seeking medical attention. Since the pain was not severe enough, 35.3% (2323/6576) of patients did not seek medical attention. Furthermore, a subgroup of respondents experiencing headache for ≥15 days were uncertain about which hospital or department to attend.ConclusionsPatients typically seek help when the pain becomes unbearable. Still, some of them did not seek medical attention while they were experiencing headache for ≥15 days per month. Therefore, it is important to raise awareness and encourage seeking early medical attention before symptoms and associated burdens become too severe to be managed effectively.