bluuebunny/crossref_metadata_2025_split huggingface dataset:
A splice donor in
E6
influences keratinocyte immortalization by beta-HPV49
Authors: Rehm Tina M. , Iftner Thomas , Stubenrauch Frank 
Published: January 2025

ABSTRACT

Human papillomaviruses (HPV) from the genus beta have been implicated in the development of cutaneous squamous cell cancer in
epidermodysplasia verruciformis
and organ transplant patients. In contrast to alpha-high-risk HPV, which cause ano-genital and oropharyngeal cancers, beta-HPV replication is not well understood. The beta-HPV49 transcriptome was analyzed by RNA sequencing using stable keratinocyte cell lines maintaining high levels of extrachromosomally replicating E8- genomes, which can be established due to a lack of the viral E8^E2 repressor protein. This analysis indicated the presence of four transcription start sites, two polyadenylation signals, and splice donor (SD) and acceptor sites consistent with the conserved gene expression patterns of animal and human PV. Surprisingly, a novel SD in the
E6
oncogene (SD217) was identified resembling the SD in
E6
of carcinogenic alpha-HPV. Mutation of SD217 enhanced E6 protein expression but had no influence on the growth of keratinocytes transduced with retroviral HPV49 E6 and E7 expression vectors. Inactivation of SD217 in the context of the HPV49 wild-type genome did not enable immortalization and prevented immortalization in the context of the E8- genome. The analysis of SD217 mutant genomes revealed a strong down-regulation of SD217 usage, but only weak effects on other viral transcripts. This suggests that SD217 does not contribute to immortalization by modulating viral gene expression. Usage of SD217 is increased in immortalized E8- cell lines compared with transiently transfected cells, which may indicate that long-term extrachromosomal maintenance requires reduced E6 protein levels.

IMPORTANCE

High-risk (hr) human papillomaviruses (HPV) from the genus alpha cause ano-genital and oropharyngeal cancers, whereas beta-HPV have been implicated to cause skin cancer in
epidermodysplasia verruciformis
and organ transplant patients. In contrast to alpha hr-HPV, the replication cycle of beta-HPV is not very well understood. Transcriptional profiling of beta-HPV49 by RNA sequencing reveals transcription start sites and splice sites conserved among HPV. Surprisingly, a splice donor site in the
E6
oncogene (SD217), previously only described for hr-HPV, was identified that controls E6 oncoprotein levels and is required for immortalization of keratinocytes by the HPV49 genome.
Autophagy-mediated TET2 degradation by ALV-J Env protein suppresses innate immune activation to promote viral replication
Authors: Chen Shihao , Wang Jiaxing , Wang Qiangzhou , Ping Yuyu , Yang Ting , Ma Kejiao , Pan Shiyu , Bi Yulin , Bai Hao , Chang Guobin 
Published: January 2025

ABSTRACT

Avian leukosis virus subgroup J (ALV-J) poses a significant threat to the poultry industry; yet, our understanding of its replication and pathogenic mechanisms is limited. The Ten-Eleven Translocation 2 (TET2) is an indispensable regulatory factor in active DNA demethylation and immune response regulation. This study reports a significant and time-dependent decrease in TET2 levels following ALV-J infection and shows that the reduction of TET2 protein is mediated by the autophagy pathway. Mechanistically, we found that the accumulation of the Env protein at the late stages of ALV-J infection triggers autophagy, which, in turn, causes the TET2 protein to be exported from the nucleus and subsequently degraded in the cytoplasm. Using CRISPR-Cas9 technology, we generated TET2-deficient chicken macrophages that exhibited increased susceptibility to ALV-J replication, which was reversed by TET2 overexpression. In addition, transcriptome analysis revealed that the absence of TET2 in chicken macrophages impairs the expression of numerous cytokines and innate immune-related genes, particularly those downregulated genes enriched in the RIG-I and Toll-like signaling pathways, leading to enhanced replication of ALV-J
in vitro
. In summary, our research identifies TET2 as an ALV-J restriction factor. However, ALV-J exploits the autophagy machinery to promote the degradation of TET2 protein, thereby disrupting the host’s innate immune responses for viral replication.

IMPORTANCE

ALV-J is a carcinogenic retrovirus that plays a critical role in avian leukosis, primarily affecting chickens. Infection with ALV-J leads to decreased production performance, compromised immune function, and the development of tumors, such as myelocytoma. Currently, there are no effective treatments for ALV-J, making the control of outbreaks a significant challenge with severe economic consequences for the poultry industry. The Env protein of ALV-J has been implicated in the virus’s pathogenicity. Our study shows that ALV-J infection induces autophagy in host cells through its Env protein, leading to the autophagic degradation of TET2, a key epigenetic regulator. The loss of TET2 in macrophages results in the downregulation of innate immune-related gene expression, thereby promoting viral replication. This is the first report to elucidate the role of the ALV-J Env protein in immune suppression
via
TET2 autophagic degradation during ALV-J infection, providing new insights into the mechanisms of viral immune evasion.
Marek’s disease virus-encoded microRNA-M6-5p facilitates viral latent infection by targeting histone demethylase KDM2B
Authors: Zhou Linyi , Zhu Runan , Jiang Bo , Cheng Jing , Liu Wenxiao , Yao Yongxiu , Li Yongqing 
Published: January 2025

ABSTRACT

Marek’s disease virus (MDV), a highly contagious and oncogenic avian alphaherpesvirus, establishes a latent infection primarily in CD4
+
T cells. Latent infections are necessary for both persistent lifelong MDV infection and viral tumorigenesis. MicroRNAs (miRNAs) play critical roles as post-transcriptional regulators of viral infections. However, the role of miRNAs in regulating MDV latency remains unclear. In this study, we found that an MDV-encoded miRNA, miR-M6-5p, inhibited viral lytic replication
in vitro
by functional screening and that infection with an MDV mutant lacking miR-M6-5p resulted in impaired MDV latency, proliferation, and tumor formation
in vivo
. Importantly, we identified lysine-specific demethylase 2b (KDM2B), an important epigenetic factor, as a target of miR-M6-5p. Furthermore, KDM2B knockdown increased the level of the transcriptionally repressive histone mark H3K27me3 on the key lytic gene pp38 promoter, accompanied by suppression of pp38 expression and reduced latent-to-lytic switch in MDV-latently infected cells, while treatment of cells with H3K27me3 inhibitors (GSK126 and Tazemetostat) markedly promoted the expression of pp38 and MDV reactivation from latency. Thus, miR-M6-5p facilitates MDV latency by epigenetically suppressing pp38 expression by targeting KDM2B. These ﬁndings unravel the mechanism by which a virus-encoded miRNA plays a critical role in the regulation of latent MDV infection.

IMPORTANCE

Similar to other herpesviruses, MDV can establish a lifelong latent infection in the host. During the latency, MDV integrates its genome into the host genome to maintain the viral genome, which is considered a prerequisite for tumor formation. Reactivation of the latent viral genome in response to intracellular and extracellular stimuli re-enters lytic replication, resulting in pathological recurrence and/or viral shedding. However, the regulatory mechanisms underlying MDV latency remain poorly understood. In the present study, we investigated the role of virus-encoded miRNAs in MDV latency. We found that miR-M6-5p facilitated MDV latency, proliferation, and tumor formation
in vivo
. Mechanistically, miR-M6-5p epigenetically suppressed the expression of the viral lytic gene pp38 by directly targeting the histone demethylase KDM2B. These ﬁndings will advance our understanding of the role of virus-encoded miRNA in the regulation of viral latency and will help guide the development of novel strategies for the effective control of MDV.
A novel neutralizing antibody recognizing a conserved conformational epitope in PDCoV S1 protein and its therapeutic efficacy in piglets
Authors: Chen Rui , Zhou Guiping , Yang Junpeng , Yuan Rong , Sun Ying , Liang Yixiao , Wu Rui , Wen Yiping , Wang Yiping , Zhao Qin , Du Senyan , Yan Qigui , Cao Sanjie , Huang Xiaobo 
Published: January 2025

ABSTRACT

Porcine deltacoronavirus (PDCoV) is an enteric pathogen that burdens the global pig industry and is a public health concern. The development of effective antiviral therapies is necessary for the prevention and control of PDCoV, yet to date, there are few studies on the therapeutic potential of PDCoV-neutralizing antibodies. Here, we investigate the therapeutic potential of a novel monoclonal antibody (mAb 4A6) which targets the PDCoV S1 protein and effectively neutralizes PDCoV, both pre- and post-attachment on cells, with IC50 values of 0.537 and 8.487 µg/mL, respectively. A phage-display peptide library was used to determine the epitope recognized by mAb 4A6, and two mimotopes, QYPVSYA (P1) and FPHWPTI (P2), were identified. KLH-P1 reacted with PDCoV-positive sera but failed to induce PDCoV-specific IgG and neutralizing antibodies in mice, suggesting P1 does not fully mimic the conformational epitope. Molecular docking and alanine scanning mutagenesis revealed that S461, P462, T463, E465, and Y467 on the S protein are essential for mAb 4A6 binding. Antibody therapy experiments in PDCoV-infected piglets showed that administering mAb 4A6 once or twice could delay the onset of diarrhea symptoms, reduce the severity of diarrhea, and decrease virus shedding. Taken together, our findings demonstrate that mAb 4A6 holds promise as a treatment against PDCoV, and the amino acids recognized by mAb 4A6 will be valuable for developing novel epitope-based vaccines or antiviral drugs.

IMPORTANCE
Porcine deltacoronavirus (PDCoV) is a novel swine enteropathogenic coronavirus that poses a potential threat to public health. Developing effective antiviral therapies is crucial for its prevention and control. Here, we demonstrated that mAb 4A6 shows promise as a treatment against PDCoV. Antibody therapy experiments conducted on PDCoV-infected piglets revealed that administering mAb 4A6 once or twice could delay the onset of diarrhea symptoms, reduce the severity of diarrhea, and decrease virus shedding. Furthermore, we characterized the conformational epitope (S461, P462, T463, E465, and Y467) recognized by mAb 4A6 through an integrated approach involving phage display peptide library, molecular docking, and alanine scanning mutagenesis. More importantly, mAb 4A6 exhibits a broad-spectrum neutralizing activity against different PDCoV strains. These findings indicate that mAb 4A6 has promising therapeutic value for PDCoV-infected piglets, and the identification of mAb 4A6 recognized epitope may provide a new idea for the identification of conformational epitopes.
The cytoplasmic tail of IBV spike mediates intracellular retention via interaction with COPI-coated vesicles in retrograde trafficking
Authors: Liang Rong , Tian Jiaxin , Liu Kangchengyin , Ma Liman , Yang Ruihua , Sun Lu , Zhao Jing , Zhao Ye , Zhang Guozhong 
Published: January 2025

ABSTRACT

Coronaviruses are characterized by their progeny assembly and budding in the endoplasmic reticulum-Golgi intermediate compartment (ERGIC). Our previous studies demonstrated that truncation of 9 amino acids in the cytoplasmic tail (CT) of the infectious bronchitis virus (IBV) spike (S) protein impairs its localization to the ERGIC, resulting in increased expression at the plasma membrane. However, the precise mechanism underlying this phenomenon remained elusive. In this study, we provide evidence that the IBV S protein could utilize coatomer protein-I (COPI)-coated vesicles for retrograde transport from the Golgi to the endoplasmic reticulum (ER). We identified the KKSV motif as the critical binding site within the CT domain of IBV S protein for COPI interaction. Further analysis reveals that IBV infection does not modulate host COPI expression. However, when COPI expression is disrupted, a higher proportion of S protein escapes to the plasma membrane. Moreover, inhibition of COPI-mediated transport during viral infection severely impairs progeny virion production and leads to increased S protein accumulation at the plasma membrane, inducing cell-cell fusion and syncytia formation. Our findings contribute to a deeper understanding of S protein intracellular trafficking during coronavirus infection, and offer valuable insights into the molecular mechanisms of viral replication and host cell biology.

IMPORTANCE

Viruses hijack or modify host cellular machiner
y
and associated pathways to facilitate their own replication. Here, we demonstrate that the infectious bronchitis virus (IBV) S protein directly interacts with coatomer protein-I (COPI)-coated vesicles through the KKSV motif in its cytoplasmic tail. COPI-coated vesicles mediate the retrograde transport of S protein from the Golgi apparatus to the endoplasmic reticulum-Golgi intermediate compartment, where viral particle assembly occurs. Our findings not only advance our understanding of IBV S protein trafficking mechanisms but also provide valuable insights for developing more effective vaccine strategies.
The combination of
Clostridium butyricum
and
Akkermansia muciniphila
mitigates DSS-induced colitis and attenuates colitis-associated tumorigenesis by modulating gut microbiota and reducing CD8
+
T cells in mice
Authors: Hua Dengxiong , Yang Qin , Li Xiaowei , Zhou Xuexue , Kang Yingqian , Zhao Yan , Wu Daoyan , Zhang Zhengrong , Li Boyan , Wang Xinxin , Qi Xiaolan , Chen Zhenghong , Cui Guzhen , Hong Wei 
Published: January 2025

ABSTRACT

The gut microbiota is closely associated with inflammatory bowel disease (IBD) and colorectal cancer (CRC). Probiotics such as
Clostridium butyricum
(CB) or
Akkermansia muciniphila
(AKK) have the potential to treat inflammatory bowel disease (IBD) or colorectal cancer (CRC). However, research on the combined therapeutic effects and immunomodulatory mechanisms of CB and AKK in treating IBD or CRC has never been studied. This study evaluates the potential of co-administration of CB and AKK in treating DSS/AOM-induced IBD and colitis-associated CRC. Our results indicate that compared to mono-administration, the co-administration of CB and AKK not only significantly alleviates symptoms such as weight loss, colon shortening, and increased Disease Activity Index in IBD mice but also regulates the gut microbiota composition and effectively suppresses colonic inflammatory responses. In the colitis-associated CRC mice model, a combination of CB and AKK significantly alleviates weight loss and markedly reduces inflammatory infiltration of macrophages and cytotoxic T lymphocytes (CTLs) in the colon, thereby regulating anti-tumor immunity and inhibiting the occurrence of inflammation-induced CRC. In addition, we found that the combined probiotic therapy of CB and AKK can enhance the sensitivity of colitis-associated CRC mice to the immune checkpoint inhibitor anti-mouse PD-L1 (aPD-L1), significantly improving the anti-tumor efficacy of immunotherapy and the survival rate of colitis-associated CRC mice. Furthermore, fecal microbiota transplantation therapy showed that transplanting feces from CRC mice treated with the co-administration of CB and AKK into other CRC mice alleviated the tumor loads in the colon and significantly extended their survival rate. Our study suggests that the combined use of two probiotics, CB and AKK, can not only alleviate chronic intestinal inflammation but also inhibit the progression to CRC. This may be a natural and relatively safe method to support the gut microbiota and enhance the host’s immunity against cancer.

IMPORTANCE
Our study suggests that the combined administration of CB and AKK probiotics, as opposed to a single probiotic strain, holds considerable promise in preventing the advancement of IBD to CRC. This synergistic effect is attributed to the ability of this probiotic combination to more effectively modulate the gut microbiota, curb inflammatory reactions, bolster the efficacy of immunotherapeutic approaches, and optimize treatment results via fecal microbiota transplantation.
Winter wheat genotype–Fusarium graminearum interactions and mycotoxin accumulation in infected spikes
Authors: McConachie Riley , Serajazari Mitra , Booker Helen 
Published: January 2025

Fusarium head blight (FHB) in wheat, caused by Fusarium graminearum (Fg), reduces yield and results in mycotoxin accumulation in the grain. Detached spikes from winter wheat varieties were inoculated with two Fg isolates and disease severity was estimated. Mycotoxin content of detached spikes was determined. Significant variety, isolate, and interaction effects were observed ( p < 0.001). FHB severity scores of varieties evaluated in an inoculated Fusarium nursery were correlated with those for detached spikes inoculated with a 3-acetyl deoxynivalenol-producing Fg isolate. Results highlight the complex interactions between Fg isolates and wheat cultivars, indicating the need for further research to better understand these relationships.
Molecularly-Imprinted Polymer-Based Electrochemical Sensor for Indirect Determination of Memantine: Greenness and Whiteness Assessment
Authors: Moaaz Eman M. , Fayed Ahmed S. , Abdel-Moety Ezzat M. , Rezk Mamdouh R. 
Published: January 2025

Substantial preference for target analytes was attained by molecularly-imprinted polymers (MIPs). A novel indirect voltammetric technique was developed to provide a useful gate for the analysis of electro-inactive substances through selective interaction with MIP and hence decrease of redox-active probe signal at the electrode’s surface. In this work, a methyldopa-based MIP was fabricated for the selective binding with memantine (MEM), a voltammetry-inactive and widely used drug for Alzheimer’s disease. In-situ electropolymerization of methyldopa monomer was implemented onto a pencil graphite electrode using MEM as a template in phosphate buffer pH 7.0. The monomer-template interaction was evaluated by UV-spectroscopy. The modified surface of the electrode was characterized using scanning electron microscope and X-ray photoelectron spectroscopy. The functionality of the sensor was assessed using cyclic voltammetry and electrochemical impedance analysis. The response was linear over a concentration range of 1.0 × 10–12 to 1.0 × 10−10 M with a detection limit down to 1.5 × 10−13 M. Sensor selectivity was studied using the co-formulated drug, donepezil. The MIP-sensor exhibited high sensitivity and proper selectivity, allowing its applicability for the analysis of MEM in combined formulations and in spiked human plasma samples. The overall process was subjected to a greenness and whiteness assessment, confirming its eco-friendliness and sustainability.
Low-Frequency Noise Characterization in UV-Sensitive Indium Tungsten Oxide Thin-Film Photodetectors via Sputtering Deposition
Authors: Yang Chih-Chiang , Chang Tzu Hsuan , Fan Yang-Ho , Huang Yu-Chun , Huang Chien-Sheng 
Published: January 2025

This study explores the deposition of indium tungsten oxide (IWO) thin films on glass substrates using sputtering techniques, with the aim of developing photodetectors sensitive to both ultraviolet (UV) and visible light spectra. The films were designed in a metal-semiconductor-metal configuration to enhance electrical conductivity, which is critical for efficient photodetection. This structure achieved a dark-to-light current ratio of 6.23 × 102 and a responsivity of 0.48 A W−1 at a reverse bias of 2 V. Furthermore, when configured as UV photodetectors, the IWO films demonstrated significant improvement, achieving a dark-to-light current ratio of 1.32 × 10⁴ under the same bias conditions. The photodetectors exhibited a detectivity (D*) of 2.18 × 1010 cm·Hz0.5·W−1 and a noise equivalent power (NEP) of 6.88 × 10−10 W. These findings highlight the potential of IWO to improve photodetector performance across different light spectra, reinforcing its viability for cost-effective integration into advanced optoelectronic devices.
Human Epidermal Growth Factor Receptor 2 Loss following Treatment with Trastuzumab Deruxtecan in Patients with Metastatic Breast Cancer
Authors: Gouda Mohamed A. , Gonugunta Amrit , Dumbrava Ecaterina E. , Yap Timothy A. , Rodon Jordi , Piha-Paul Sarina A. , Pohlmann Paula R. , Damodaran Senthil , Murthy Rashmi , Valero Vicente , Mouabbi Jason A. , Tripathy Debasish , Sahin Aysegul A. , Chen Hui , Meric-Bernstam Funda 
Published: January 2025

Abstract

Purpose:
Trastuzumab deruxtecan (T-DXd) is currently approved for treating metastatic breast cancer (MBC) that is HER2 positive [immunohistochemistry (IHC) score of 3+ or in situ hybridization (ISH) positivity] or HER2-low (IHC score of 1+ or IHC 2+/ISH negative), as well as for HER2-positive gastric cancer, HER2-mutant lung cancer, and HER2-overexpressing solid tumors. Given the increasing utilization of T-DXd, we sought to determine how HER2 status might change following T-DXd therapy.

Experimental Design:
We retrospectively reviewed patients with MBC who received T-DXd at the University of Texas MD Anderson Cancer Center. We included patients with paired pre- and post-treatment biopsies assessed for HER2 status using IHC.

Results:
We included 41 patients with MBC who received treatment with T-DXd and had paired pre- and post-treatment biopsies assessed for HER2 status using IHC. HER2 loss was observed in 11 patients [32.4% of 34 patients with pre-treatment HER2 expression (1+, 2+, or 3+)] following treatment with T-DXd. In addition to the 11 patients with HER2 loss, another 10 patients (29.4%) had a decrease in HER2 score after treatment with T-DXd.

Conclusions:
HER2 loss and decrease in HER2 expression are common in patients with MBC receiving treatment with T-DXd. Reevaluation of HER2 status following T-DXd treatment should be considered prior to alternate HER2-targeted therapies that require HER2 overexpression for efficacy.
Similar trajectories of psychological states predict marital
satisfaction
Authors: Li Lei , Huang Xinyue , Zheng Qingyu , Xiao Jinming , Shan Xiaolong , Chen Huafu , Duan Xujun 
Published: January 2025

Abstract
Modern mate selection theories suggest that people are more likely to marry someone similar to themselves in terms of numerous attributes. Recent research has demonstrated a positive relationship between marital satisfaction and inter-subject correlation (ISC) of neural responses while viewing movies in married couples. Nevertheless, conventional ISC methods solely capture information about similarity in the temporal evolution of region-averaged neural responses, disregarding nuanced spatially distributed response topographies. Here, we integrated ISC and multi-voxel pattern (MVP) analysis to capitalize inter-subject trajectory similarity (ISTS) of MVP. We demonstrated that married couples showed significantly higher ISTS than randomly selected pairs, during movie viewing and resting state. The ISTS was particularly positively associated with marital satisfaction in married couples while viewing movies. In order to investigate latent “psychological states” characterized by relatively stable patterns of MVP, a hidden Markov model was used to segment the neural events in married couples during viewing movies. We found the ISTS within manually defined events was a strong predictor of marital satisfaction. These results suggest that married couples with high-level marital satisfaction may experience similar trajectories of mental states when exposed to a common marital-related stimulus, and extend our understanding of the neurobiological signatures of intimate relationship.