bluuebunny/crossref_metadata_2025_split huggingface dataset:
A multi-epitope/CXCL11 prime/pull coronavirus mucosal vaccine boosts the frequency and the function of lung-resident memory CD4
+
and CD8
+
T cells and enhanced protection against COVID-19-like symptoms and death caused by SARS-CoV-2 infection
Authors: Zayou Latifa , Prakash Swayam , Dhanushkodi Nisha Rajeswari , Quadiri Afshana , Ibraim Izabela Coimbra , Singer Mahmoud , Salem Amirah , Shaik Amin Mohammed , Suzer Berfin , Chilukuri Amruth , Tran Jennifer , Nguyen Pauline Chau , Sun Miyo , Hormi-Carver Kathy K. , Belmouden Ahmed , Vahed Hawa , Gil Daniel , Ulmer Jeffrey B. , BenMohamed Lbachir 
Published: December 2023

ABSTRACT

The pandemic of the coronavirus disease 2019 (COVID-19) has created the largest global health crisis in almost a century. Low frequencies of functional SARS-CoV-2-specific CD4
+
and CD8
+
T cells in the lungs of COVID-19 patients have been associated with severe cases of COVID-19. Low levels of T cell-attracting CXCL9, CXCL10, and CXCL11 chemokines in infected lungs may not be sufficient for the migration of CD4
+
and CD8
+
T cells from circulation into infected lungs. We hypothesize that a coronavirus vaccine strategy that boosts the frequencies of functional SARS-CoV-2-specific CD4
+
and CD8
+
T cells in the lungs would lead to better protection from COVID-19-like symptoms. In the present study, we designed and pre-clinically tested the safety, immunogenicity, and protective efficacy of a novel multi-epitope/CXCL11 prime/pull mucosal coronavirus vaccine. This prime/pull vaccine strategy consists of intranasal delivery of a lung-tropic adeno-associated virus type 9 vector that incorporates highly conserved human CD4
+
and CD8
+
cell epitopes of SARS-CoV-2 (
prime
) followed by recruitment of the primed T cells into the lungs using the T cell-attracting chemokine, CXCL-11 (
pull
). We demonstrated that the immunization of HLA-DR*0101/HLA-A*0201/hACE2 triple transgenic mice with this multi-epitope/CXCL11 prime/pull coronavirus mucosal vaccine: (i) increased the frequencies of functional CD4
+
and CD8
+
T
EM
, T
CM
, and T
RM
cells in the lungs and (ii) reduced COVID-19-like symptoms, lowered virus replication, and prevented deaths following challenge with SARS-CoV-2. These findings demonstrate that bolstering the number of functional lung-resident memory CD4
+
and CD8
+
T cells improved protection against SARS-CoV-2 infection, COVID-19-like symptoms, and death.

IMPORTANCE

Although the current rate of SARS-CoV-2 infections has decreased significantly, COVID-19 still ranks very high as a cause of death worldwide. As of October 2023, the weekly mortality rate is still at 600 deaths in the United States alone, which surpasses even the worst mortality rates recorded for influenza. Thus, the long-term outlook of COVID-19 is still a serious concern outlining the need for the next-generation vaccine. This study found that a prime/pull coronavirus vaccine strategy increased the frequency of functional SARS-CoV-2-specific CD4
+
and CD8
+
memory T cells in the lungs of SARS-CoV-2-infected triple transgenic HLA-DR*0101/HLA-A*0201/hACE2 mouse model, thereby resulting in low viral titer and reduced COVID-19-like symptoms.
Joint application of metagenomic next-generation sequencing and histopathological examination for the diagnosis of pulmonary infectious disease
Authors: Yang Linhui , Wang Kaige , Li Yalun , Li Weimin , Liu Dan 
Published: December 2023

ABSTRACT
The diagnosis of some pulmonary infectious diseases and their pathogens is very difficult. We clarified the diagnostic value of the joint application of metagenomic next-generation sequencing (mNGS) and histopathological examination for the diagnosis of pulmonary infectious diseases in this study. We retrospectively enrolled 108 patients with infectious and noninfectious diseases who visited the West China Hospital of Sichuan University from January 2019 to June 2022. Pathogens in core needle biopsy tissue were detected using mNGS and traditional pathological examination. The diagnostic accuracy of the combined mNGS and histopathology protocol for pulmonary infectious diseases was contrasted with that of histopathological examination alone. The area under the receiver operating characteristic curve (ROC curve) of mNGS combined with histopathological examination was 0.840 for pulmonary infectious diseases, and the area under the ROC curve of histopathological examination alone was 0.644. The areas under the ROC curve of mNGS combined with histopathological examination for pulmonary fungal infection, pulmonary tuberculosis, and lung abscess were 0.876, 0.875, and 0.840, respectively. In pulmonary infectious diseases, the areas under the ROC curve of histopathological examination alone for the above three types of pulmonary infections were 0.760, 0.719, and 0.575, respectively. For pulmonary infectious diseases, a joint application of metagenomic next-generation sequencing and histopathological examination can not only be used for differential diagnosis but also increase the positive rate of pathogen identification compared with histopathological examination alone, especially for rare pathogen infections.

IMPORTANCE
The diagnosis of some pulmonary infectious diseases and their pathogens is very difficult. A more precise diagnosis of pulmonary infectious diseases can help clinicians use proper antibiotics as well as reduce the development of drug-resistant bacteria. In this study, we performed both mNGS and pathology on lung puncture biopsy tissue from patients and found that combined mNGS and histopathology testing was significantly more effective than histopathology testing alone in detecting infectious diseases and identifying infectious diseases. In addition, the combined approach improves the detection rate of pathogenic microorganisms in infectious diseases and can be used to guide precision clinical treatment.
The induced and intrinsic resistance of
Escherichia coli
to sanguinarine is mediated by AcrB efflux pump
Authors: Dai Jian-Sheng , Xu Jian , Shen Hao-Jie , Chen Ni-Pi , Zhu Bing-Qi , Xue Zheng-Jie , Chen Hao-Han , Ding Zhi-Shan , Ding Rui , Qian Chao-Dong 
Published: December 2023

ABSTRACT

Sanguinarine-containing phytobiotic is becoming increasingly popularly utilized as antibiotic alternatives in animal production. However, their potential risks to the human health and environment remain poorly understood. The present study aims to evaluate the occurrence of drug resistance in
Escherichia coli
after treatment with sanguinarine and investigate the molecular basis associated with sanguinarine resistance. Repetitive exposure of
E. coli
to subinhibitory dose of this phytochemical selected for mutants within genes encoding AcrR or MarR, transcriptional regulators of the multidrug tripartite efflux pump AcrAB-TolC. Disruption of the gene
acrB
caused a 16-fold MIC decrease for sanguinarine against
E. coli
strains, while the susceptibility of
acrB
-deficient mutants to sanguinarine was restored in complemented strains with ectopically expressed
acrB
. Accumulation assays suggested that the high susceptibility of
acrB
-deficient mutants was a consequence of a decrease in drug efflux. Consistent with this, the antibacterial activity of sanguinarine against wild-type (WT) strains of
E. coli
was significantly strengthened by combining it with 1-(1-naphthylmethyl)-piperazine (NMP), a classical efflux pump inhibitor. In addition, the combination of
in silico
prediction, competitive inhibition assay, and functional analysis of AcrB variants led to the identification of sanguinarine as a CH3-preferring substrate of AcrB, which could partly explain the selectively enhanced antibacterial effect of NMP on sanguinarine.

IMPORTANCE

The use of plant extracts is increasing as an alternative to synthetic compounds, especially antibiotics. However, there is no sufficient knowledge on the mechanisms and potential risks of antibiotic resistance induced by these phytochemicals. In the present study, we found that stable drug resistant mutants of
E. coli
emerged after repetitive exposure to sanguinarine and demonstrated that the AcrB efflux pump contributed to the emerging of induced and intrinsic resistance of
E. coli
to this phytochemical. Our results offered some insights into comprehending and preventing the onset of drug-resistant strains when utilizing products containing sanguinarine.
Hsa-LINC02418/mmu-4930573I07Rik regulated by METTL3 dictates anti-PD-L1 immunotherapeutic efficacy via enhancement of Trim21-mediated PD-L1 ubiquitination
Authors: Sun Zhijia , Mai Haixing , Xue Chunyuan , Fan Zhongyi , Li Jiangbo , Chen Hairui , Huo Nan , Kang Xiaofeng , Tang Chuanhao , Fang Liaoxin , Zhao Hui , Han Yuchen , Sun Chao , Peng Huanyan , Du Yimeng , Yang Jing , Du Nan , Xu Xiaojie 
Published: December 2023

BackgroundLimited response to programmed death ligand-1 (PD-L1)/programmed death 1 (PD-1) immunotherapy is a major hindrance of checkpoint immunotherapy in non-small cell lung cancer (NSCLC). The abundance of PD-L1 on the tumor cell surface is crucial for the responsiveness of PD-1/PD-L1 immunotherapy. However, the negative control of PD-L1 expression and the physiological significance of the PD-L1 inhibition in NSCLC immunotherapy remain obscure.MethodsBioinformatics analysis was performed to profile and investigate the long non-coding RNAs that negatively correlated with PD-L1 expression and positively correlated with CD8+T cell infiltration in NSCLC. Immunofluorescence,in vitroPD-1 binding assay, T cell-induced apoptosis assays andin vivosyngeneic mouse models were used to investigate the functional roles of LINC02418 and mmu-4930573I07Rik in regulating anti-PD-L1 therapeutic efficacy in NSCLC. The molecular mechanism of LINC02418-enhanced PD-L1 downregulation was explored by immunoprecipitation, RNA immunoprecipitation (RIP), and ubiquitination assays. RIP, luciferase reporter, and messenger RNA degradation assays were used to investigate the m6A modification of LINC02418 or mmu-4930573I07Rik expression. Bioinformatics analysis and immunohistochemistry (IHC) verification were performed to determine the significance of LINC02418, PD-L1 expression and CD8+T cell infiltration.ResultsLINC02418 is a negative regulator of PD-L1 expression that positively correlated with CD8+T cell infiltration, predicting favorable clinical outcomes for patients with NSCLC. LINC02418 downregulates PD-L1 expression by enhancing PD-L1 ubiquitination mediated by E3 ligase Trim21. Both hsa-LINC02418 and mmu-4930573I07Rik (its homologous RNA in mice) regulate PD-L1 therapeutic efficacy in NSCLC via Trim21, inducing T cell-induced apoptosisin vitroandin vivo. Furthermore, METTL3 inhibition via N6-methyladenosine (m6A) modification mediated by YTHDF2 reader upregulates hsa-LINC02418 and mmu-4930573I07Rik. In patients with NSCLC, LINC02418 expression is inversely correlated with PD-L1 expression and positively correlated with CD8+T infiltration.ConclusionLINC02418 functions as a negative regulator of PD-L1 expression in NSCLC cells by promoting the degradation of PD-L1 through the ubiquitin-proteasome pathway. The expression of LINC02418 is regulated by METTL3/YTHDF2-mediated m6A modification. This study illuminates the underlying mechanisms of PD-L1 negative regulation and presents a promising target for improving the effectiveness of anti-PD-L1 therapy in NSCLC.
The Realities of Evaluating Educational Technology in School Settings
Authors: Venn-Wycherley Megan , Kharrufa Ahmed , Lechelt Susan , Nicholson Rebecca , Howland Kate , Almjally Abrar , Trory Anthony , Sarangapani Vidya 
Published: December 2023

HCI researchers are increasingly interested in the evaluation of educational technologies in context, yet acknowledge that challenges remain regarding the logistical, material and methodological constraints of this approach to research [
18
,
53
].

Through the analysis of the authors’ contributed thematic research vignettes, the following article exposes the practical realities of evaluating educational technologies in school settings. This includes insights into the planning stages of evaluation, the relationship between the researcher and the school environment, and the impact of the school context on the data collection process.
We conclude by providing an orientation for the design of HCI educational technology research undertaken in school contexts, providing guidance such as considering the role of modular research design, clarifying goals and expectations with school partners, and reporting researcher positionality.
Neurotransmitter Receptor HTR2B Regulates Lipid Metabolism to Inhibit Ferroptosis in Gastric Cancer
Authors: Tu Ru-Hong , Wu Sheng-Ze , Huang Ze-Ning , Zhong Qing , Ye Yin-Hua , Zheng Chao-Hui , Xie Jian-Wei , Wang Jia-Bin , Lin Jian-Xian , Chen Qi-Yue , Huang Chang-Ming , Lin Mi , Lu Jun , Cao Long-Long , Li Ping 
Published: December 2023

Abstract

Nerves can support tumor development by secreting neurotransmitters that promote cancer cell proliferation and invasion. 5-Hydroxytryptamine (5-HT) is a critical neurotransmitter in the gastrointestinal nervous system, and 5-HT signaling has been shown to play a role in tumorigenesis. Here, we found that expression of the 5-HT receptor HTR2B was significantly elevated in human gastric adenocarcinoma tissues compared with nontumor tissues, and high HTR2B expression corresponded to shorter patient survival. Both 5-HT and a specific HTR2B agonist enhanced gastric adenocarcinoma cell viability under metabolic stress, reduced cellular and lipid reactive oxygen species, and suppressed ferroptosis; conversely, HTR2B loss or inhibition with a selective HTR2B antagonist yielded the inverse tumor suppressive effects. In a patient-derived xenograft tumor model, HTR2B-positive tumors displayed accelerated growth, which was inhibited by HTR2B antagonists. Single-cell analysis of human gastric adenocarcinoma tissues revealed enrichment of PI3K/Akt/mTOR and fatty acid metabolism–related gene clusters in cells expressing HTR2B compared with HTR2B-negative cells. Mechanistically, HTR2B cooperated with Fyn to directly regulate p85 activity and trigger the PI3K/Akt/mTOR signaling pathway, which led to increased expression of HIF1α and ABCD1 along with decreased levels of lipid peroxidation and ferroptosis. Together, these findings demonstrate that HTR2B activity modulates PI3K/Akt/mTOR signaling to stimulate gastric cancer cell survival and indicate that HTR2B expression could be a potential prognostic biomarker in patients with gastric cancer.

Significance:
Nerve cancer cross-talk mediated by HTR2B inhibits lipid peroxidation and ferroptosis in gastric cancer cells and promotes viability under metabolic stress, resulting in increased tumor growth and decreased patient survival.
Osteoclast Cancer Cell Metabolic Cross-talk Confers PARP Inhibitor Resistance in Bone Metastatic Breast Cancer
Authors: Fan Huijuan , Xu Zhanao , Yao Ke , Zheng Bingxin , Zhang Yuan , Wang Xuxiang , Zhang Tengjiang , Li Xuan , Hu Haitian , Yue Bin , Hu Zeping , Zheng Hanqiu 
Published: December 2023

Abstract

The majority of patients with late-stage breast cancer develop distal bone metastases. The bone microenvironment can affect response to therapy, and uncovering the underlying mechanisms could help identify improved strategies for treating bone metastatic breast cancer. Here, we observed that osteoclasts reduced the sensitivity of breast cancer cells to DNA damaging agents, including cisplatin and the PARP inhibitor (PARPi) olaparib. Metabolic profiling identified elevated glutamine production by osteoclasts. Glutamine supplementation enhanced the survival of breast cancer cells treated with DNA damaging agents, while blocking glutamine uptake increased sensitivity and suppressed bone metastasis. GPX4, the critical enzyme responsible for glutathione oxidation, was upregulated in cancer cells following PARPi treatment through stress-induced ATF4-dependent transcriptional programming. Increased glutamine uptake and GPX4 upregulation concertedly enhanced glutathione metabolism in cancer cells to help neutralize oxidative stress and generate PARPi resistance. Analysis of paired patient samples of primary breast tumors and bone metastases revealed significant induction of GPX4 in bone metastases. Combination therapy utilizing PARPi and zoledronate, which blocks osteoclast activity and thereby reduces the microenvironmental glutamine supply, generated a synergistic effect in reducing bone metastasis. These results identify a role for glutamine production by bone-resident cells in supporting metastatic cancer cells to overcome oxidative stress and develop resistance to DNA-damaging therapies.

Significance:
Metabolic interaction between osteoclasts and tumor cells contributes to resistance to DNA-damaging agents, which can be blocked by combination treatment with PARP and osteoclast inhibitors to reduce bone metastatic burden.
New T-Cell Therapies for Brain Metastasis, CD133 in the Driver's Seat
Authors: Sloan Anthony R. , Thapliyal Mihika , Lathia Justin D. 
Published: December 2023

Summary
Chimeric antigen receptor (CAR)-T cell immunotherapy has revolutionized cancer therapy for some advanced cancers, but success is predicated on identifying the correct cell surface target. In a recent article, the authors leveraged the cancer stem cell surface antigen CD133 to develop a CAR-T therapy for brain metastasis.
See related article by Kieliszek et al., p. 554
Abstract A001: Mapping the interaction between C-type lectin domain group 14A and Multimerin 2
Authors: Baber Aleen , Birmingham Victoria L , Bicknell Roy , Morrison Philip R 
Published: December 2023

Abstract
Introduction: Understanding the molecular basis of protein-protein interactions involved in the regulation of angiogenesis enhances our understanding of cancer pathogenesis and enables the development of novel anti-cancer therapies. In this study, we focused on the transmembrane spanning glycoprotein C-type lectin domain group 14A (CLEC14A), which is exclusively expressed on the tumor endothelium and is important in regulating tumor growth. CLEC14A promotes endothelial tube formation and migration in vitro, in addition tumor growth is retarded in CLEC14A knockout mice. CLEC14A, through its N-terminal C-type lectin domain (CTLD) interacts with the extracellular matrix protein Multimerin 2 (MMRN2) and heparan sulfate proteoglycans. Administration of antibodies which block the CLEC14A-MMRN2 interaction decreases tumor growth in vivo indicating the importance of this interaction, however the biological significance of CLEC14A’s binding to heparan sulfate proteoglycans is not known.
Aims: The purpose of this study was to identify the area and key residues on CLEC14A which interact directly with MMRN2. Mapping the CLEC14A-MMRN2 interface would enable the design of small molecule inhibitors of this interaction, a potential anti-cancer strategy.
Methods: We employed the Alpha fold predictive modelling algorithm to analyze the predicted structure of CLEC14A. Solvent-facing residues within a previously identified critical loop region were mutated to alanine and binding to MMRN2 was determined. Flow cytometry was used to assess the cell surface expression of these CLEC14A mutants, and far western blotting was employed to determine their capacity to bind MMRN2. Furthermore, we studied whether these mutants interacted with heparin-bound agarose beads in pulldown assays.
Results: The alanine-scanning approach resulted in the identification of specific residues of CLEC14A which directly interacted with MMRN2. Furthermore, we identified the epitope on CLEC14A for a biologically active antibody previously reported to block the CLEC14A-MMRN2 interaction. Additionally, we identified critical residues that are essential for cell surface trafficking of CLEC14A. Importantly, the CLEC14A mutants that do not bind to MMRN2 retain their capacity to bind heparin.
Conclusion: By leveraging predictive modelling software, we have characterized the molecular interaction between CLEC14A and MMRN2. Our findings may inform anti-angiogenesis drug design in the future.
Citation Format: Aleen Baber, Victoria L Birmingham, Roy Bicknell, Philip R Morrison. Mapping the interaction between C-type lectin domain group 14A and Multimerin 2 [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A001.
Abstract A019: eIF4A and PDCD4 expression in TNBC underlies sensitivity to natural product translation inhibitor
Authors: Subramanian Alagu , Xue Haoran , Hull Kenneth G , Romo Daniel , Taube Joseph 
Published: December 2023

Abstract
Despite recent advances in immunotherapy and adjuvant-therapy, resistance to cancer therapeutics is common and requires novel approaches. Moreover, highly aggressive triple-negative breast cancers lack effective targeted treatments. Deregulation of translation factors is associated with the increased proliferation of TNBC cells, heightened CSC activity, and poor patient outcomes. Thus targeting translation regulatory factors upregulated in TNBC is a promising approach to developing novel treatments. Pateamine A (PatA), a natural marine macrodiolide product, inhibits RNA cap-dependent translation by binding and sequestering the eukaryotic translation initiation factor eIF4A. eIF4A promotes the translation of polypurine-rich mRNA sequences, which are enriched within breast cancer oncogenes. Here we report the anticancer efficacy of novel PatA analogs we have synthesized against breast cancer cell lines. The PatA analogs exhibited selective cytotoxicity to breast and colorectal cancers compared to non-cancerous cells measured by Cell Titer-Blue viability studies. Novel analogs show greater antiproliferative potency against models of triple-negative than against human mammary epithelial cells (HMLE). To further elucidate eIF4A as a molecular target, we conducted analyses of patient tissue samples in the Cancer Genome Atlas (TCGA). Our analyses reveal the overexpression of eIF4A in tumor tissues compared to normal tissues and gene correlation studies reveal the upregulation of key co-expressed tumor drivers including beta-catenin, fibronectin, and epithelial-to-mesenchymal transition (EMT) markers such as SNAIL and SLUG. Further analyses show a downregulation of tumor suppressor protein PDCD4, an endogenous inhibitor of eIF4A, in cancer tissues. We have generated eIF4A shRNA knockdown and PDCD4 shRNA knockdown cell lines to uncover the eIF4A-PDCD4 regulatory axis across breast adenocarcinoma and colorectal adenocarcinoma cell types. We show that the loss of eIF4A attenuates the mesenchymal and stem-like phenotype of breast cancer stem cells revealed by phenotypic assays. Our results suggest that targeting translation initiator eIF4A is an effective approach against highly proliferative and metastatic breast cancer types. The presented findings underscore the potential of eIF4A as a promising molecular target and supports translational control as a viable approach against aggressive cancers.
Citation Format: Alagu Subramanian, Haoran Xue, Kenneth G Hull, Daniel Romo, Joseph Taube. eIF4A and PDCD4 expression in TNBC underlies sensitivity to natural product translation inhibitor [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A019.