bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immune marker expression of irradiated mesothelioma cell lines
Authors: Chang Faith , Keam Synat , Hoang Tracy Seymour , Creaney Jenette , Gill Suki , Nowak Anna K. , Ebert Martin , Cook Alistair M. 
Published: October 2022

BackgroundThough immune checkpoint inhibition has recently shown encouraging clinical efficacy in mesothelioma, most patients do not respond. Combining immune checkpoint inhibition with radiotherapy presents an attractive option for improving treatment responses owing to the various immunomodulatory effects of radiation on tumors. However, the ideal dosing and scheduling of combined treatment remains elusive, as it is poorly studied in mesothelioma. The present study characterizes the dose- and time-dependent changes to expression of various immune markers and cytokines important to antitumor responses following irradiation of mesothelioma cell lines.MethodsTwo murine (AB1, AE17) and two human (BYE, JU77) mesothelioma cell lines were treated with titrated gamma-radiation doses (1-8 Gy) and the expression of MHC class-I, MHC class-II and PD-L1 was measured over a series of post-irradiation timepoints (1-72 hours) by flow cytometry. Levels of cytokines IL-1α, IL-1β, IL-6, IL-10, IL-12p70, IL-17A, IL-23, IL-27, MCP-1, IFN-β, IFN-γ, TNF-α, and GM-CSF were measured by multiplex immunoassay in murine cell lines following 8 Gy radiation.ResultsFollowing irradiation, a dose-dependent upregulation of MHC-I and PD-L1 was observed on three of the four cell lines studied to varying extents. For all cell lines, the increase in marker expression was most pronounced 72 hours after radiation. At this timepoint, increases in levels of cytokines IFN-β, MCP-1 and IL-6 were observed following irradiation with 8 Gy in AB1 but not AE17, reflecting patterns in marker expression.ConclusionsOverall, this study establishes the dose- and time-dependent changes in immune marker expression of commonly studied mesothelioma cell lines following radiation and will inform future study into optimal dosing and scheduling of combined radiotherapy and immune checkpoint inhibition for mesothelioma.
Development and validation of prognostic models for colon adenocarcinoma based on combined immune-and metabolism-related genes
Authors: Jiang Hui-zhong , Yang Bing , Jiang Ya-li , Liu Xun , Chen Da-lin , Long Feng-xi , Yang Zhu , Tang Dong-xin 
Published: October 2022

BackgroundThe heterogeneity of tumor tissue is one of the reasons for the poor effect of tumor treatment, which is mainly affected by the tumor immune microenvironment and metabolic reprogramming. But more research is needed to find out how the tumor microenvironment (TME) and metabolic features of colon adenocarcinoma (COAD) are related.MethodsWe obtained the transcriptomic and clinical data information of COAD patients from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Consensus clustering analysis was used to identify different molecular subtypes, identify differentially expressed genes (DEGs) associated with immune-and metabolism-related genes (IMRGs) prognosis. Univariate and multivariable Cox regression analysis and Lasso regression analysis were applied to construct the prognostic models based on the IMRG risk score. The correlations between risk scores and TME, immune cell infiltration, and immune checkpoint genes were investigated. Lastly, potential appropriate drugs related to the risk score were screened by drug sensitivity analysis.ResultsBy consensus clustering analysis, we identified two distinct molecular subtypes. It was also found that the multilayered IMRG subtypes were associated with the patient’s clinicopathological characteristics, prognosis, and TME cell infiltration characteristics. Meanwhile, a prognostic model based on the risk score of IMRGs was constructed and its predictive power was verified internally and externally. Clinicopathological analysis and nomogram give it better clinical guidance. The IMRG risk score plays a key role in immune microenvironment infiltration. Patients in the high-risk groups of microsatellite instability (MSI) and tumor mutational burden (TMB) were found to, although with poor prognosis, actively respond to immunotherapy. Furthermore, IMRG risk scores were significantly associated with immune checkpoint gene expression. The potential drug sensitivity study helps come up with and choose a chemotherapy treatment plan.ConclusionOur comprehensive analysis of IMRG signatures revealed a broad range of regulatory mechanisms affecting the tumor immune microenvironment (TIME), immune landscape, clinicopathological features, and prognosis. And to explore the potential drugs for immunotherapy. It will help to better understand the molecular mechanisms of COAD and provide new directions for disease treatment.
Activity and rational combinations of a novel, engineered chimeric, TRAIL-based ligand in diffuse large B-cell lymphoma
Authors: Piechna Karolina , Żołyniak Aleksandra , Jabłońska Ewa , Noyszewska-Kania Monika , Szydłowski Maciej , Żerek Bartłomiej , Kulecka Maria , Rumieńczyk Izabela , Mikula Michał , Juszczyński Przemysław 
Published: October 2022

BackgroundTRAIL (TNF-related apoptosis inducing ligand) exhibits selective proapoptotic activity in multiple tumor types, while sparing normal cells. This selectivity makes TRAIL an attractive therapeutic candidate. However, despite encouraging activity in preclinical models, clinical trials with TRAIL mimetics/death receptor agonists demonstrated insufficient activity, largely due to emerging resistance to these agents. Herein, we investigated the cytotoxic activity of a novel, TRAIL-based chimeric protein AD-O51.4 combining TRAIL and VEGFA-derived peptide sequences, in hematological malignancies. We characterize key molecular mechanisms leading to resistance and propose rational pharmacological combinations sensitizing cells to AD-O51.4.MethodsSensitivity of DLBCL, classical Hodgkin lymphoma, (cHL), Burkitt lymphoma (BL) and acute myeloid leukemia (AML) to AD-O51.4 was assessed in vitro with MTS assay and apoptosis tests (Annexin V/PI staining). Markers of apoptosis were assessed using immunoblotting, flow cytometry or fluorogenic caspase cleavage assays. Resistant cell lines were obtained by incubation with increasing doses of AD-O51.4. Transcriptomic analyses were performed by RNA sequencing. Sensitizing effects of selected pathway modulators (BCL2, dynamin and HDAC inhibitors) were assessed using MTS/apoptosis assays.ResultsAD-O51.4 exhibited low-nanomolar cytotoxic activity in DLBCL cells, but not in other lymphoid or AML cell lines. AD-O51.4 induced death-receptor (DR) mediated, caspase-dependent apoptosis in sensitive DLBCL cells, but not in primary resistant cells. The presence of DRs and caspase 8 in cancer cells was crucial for AD-O51.4-induced apoptosis. To understand the potential mechanisms of resistance in an unbiased way, we engineered AD-O51.4-resistant cells and evaluated resistance-associated transcriptomic changes. Resistant cells exhibited changes in the expression of multiple genes and pathways associated with apoptosis, endocytosis and HDAC-dependent epigenetic reprogramming, suggesting potential therapeutic strategies of sensitization to AD-O51.4. In subsequent analyses, we demonstrated that HDAC inhibitors, BCL2 inhibitors and endocytosis/dynamin inhibitors sensitized primary resistant DLBCL cells to AD-O51.4.ConclusionsTaken together, we identified rational pharmacologic strategies sensitizing cells to AD-O51.4, including BCL2, histone deacetylase inhibitors and dynamin modulators. Since AD-O51.4 exhibits favorable pharmacokinetics and an acceptable safety profile, its further clinical development is warranted. Identification of resistance mechanisms in a clinical setting might indicate a personalized pharmacological approach to override the resistance.
Impact of perioperative blood transfusion on long-term survival in patients with different stages of perihilar cholangiocarcinoma treated with curative resection: A multicentre propensity score matching study
Authors: Liu Zhi-Peng , Cheng Zheng-Jun , Dai Hai-Su , Zhong Shi-Yun , Zhao Dong-Chu , Gong Yi , Zuo Jing-Hua , Che Xiao-Yu , Chen Wei-Yue , Wang Zi-Ran , Yu Ting , Cheng Jun-Jie , Liu Xing-Chao , Bai Jie , Jiang Yan , Zhang Yan-Qi , Lau Wan Yee , Deng Shi-Quan , Chen Zhi-Yu 
Published: October 2022

Background &amp; aimThe association of perioperative blood transfusion (PBT) with long-term survival in perihilar cholangiocarcinoma (pCCA) patients after surgical resection with curative intent is controversial and may differ among different stages of the disease. This study aimed to investigate the impact of PBT on long-term survival of patients with different stages of pCCA.MethodsConsecutive pCCA patients from three hospitals treated with curative resection from 2012 to 2019 were enrolled and divided into the PBT and non-PBT groups. Propensity score matching (PSM) was used to balance differences in baseline characteristics between the PBT and non-PBT groups. Kaplan–Meier curves and log-rank test were used to compare overall survival (OS) and recurrence-free survival (RFS) between patients with all tumor stages, early stage (8th AJCC stage I), and non-early stage (8th AJCC stage II-IV) pCCA in the PBT and non-PBT groups. Cox regression analysis was used to determine the impact of PBT on OS and RFS of these patients.Results302 pCCA patients treated with curative resection were enrolled into this study. Before PSM, 68 patients (22 patients in the PBT group) were in the early stage and 234 patients (108 patients in the PBT group) were in the non-early stage. Patients with early stage pCCA in the PBT group had significantly lower OS and RFS rates than those in the non-PBT group. However, there were with no significant differences between the 2 groups with all tumor stages and non-early stage pCCA. After PSM, there were 18 matched pairs of patients with early stage and 72 matched pairs of patients with non-early stage. Similar results were obtained in the pre- and post-PSM cohorts: patients with early stage pCCA in the PBT group showed significantly lower OS and RFS rates than those in the non-PBT group, but there were no significant differences between the 2 groups for patients with all tumor stages and non-early stage pCCA. Cox regression analysis demonstrated that PBT was independently associated with worse OS and RFS for patients with early stage pCCA.ConclusionsPBT had a negative impact on long-term survival in patients with early stage pCCA after curative resection, but not in patients with non-early stage pCCA.
MC-ViT: Multi-path cross-scale vision transformer for thymoma histopathology whole slide image typing
Authors: Zhang Huaqi , Chen Huang , Qin Jin , Wang Bei , Ma Guolin , Wang Pengyu , Zhong Dingrong , Liu Jie 
Published: October 2022

ObjectivesAccurate histological typing plays an important role in diagnosing thymoma or thymic carcinoma (TC) and predicting the corresponding prognosis. In this paper, we develop and validate a deep learning-based thymoma typing method for hematoxylin &amp; eosin (H&amp;E)-stained whole slide images (WSIs), which provides useful histopathology information from patients to assist doctors for better diagnosing thymoma or TC.MethodsWe propose a multi-path cross-scale vision transformer (MC-ViT), which first uses the cross attentive scale-aware transformer (CAST) to classify the pathological information related to thymoma, and then uses such pathological information priors to assist the WSIs transformer (WT) for thymoma typing. To make full use of the multi-scale (10×, 20×, and 40×) information inherent in a WSI, CAST not only employs parallel multi-path to capture different receptive field features from multi-scale WSI inputs, but also introduces the cross-correlation attention module (CAM) to aggregate multi-scale features to achieve cross-scale spatial information complementarity. After that, WT can effectively convert full-scale WSIs into 1D feature matrices with pathological information labels to improve the efficiency and accuracy of thymoma typing.ResultsWe construct a large-scale thymoma histopathology WSI (THW) dataset and annotate corresponding pathological information and thymoma typing labels. The proposed MC-ViT achieves the Top-1 accuracy of 0.939 and 0.951 in pathological information classification and thymoma typing, respectively. Moreover, the quantitative and statistical experiments on the THW dataset also demonstrate that our pipeline performs favorably against the existing classical convolutional neural networks, vision transformers, and deep learning-based medical image classification methods.ConclusionThis paper demonstrates that comprehensively utilizing the pathological information contained in multi-scale WSIs is feasible for thymoma typing and achieves clinically acceptable performance. Specifically, the proposed MC-ViT can well predict pathological information classes as well as thymoma types, which show the application potential to the diagnosis of thymoma and TC and may assist doctors in improving diagnosis efficiency and accuracy.
Thymic cyst: Is attenuation artifactually increased on contrast-enhanced CT?
Authors: Wang Chao , Mao Jin , Yang Siyu , Xie Huanhuan , Wang Shan , Hu Ling 
Published: October 2022

BackgroundThymic cysts are often misinterpreted as thymomas or lymph nodes, then leading to unnecessary thymectomy. The purpose of this study was to investigate how the adjacent large vessels artifactually affected attenuation values of thymic cysts on contrast–enhanced CT (CE-CT).MethodsIn this retrospective study, a total of 84 patients were included with pathological diagnosis of thymic cysts and preoperative CE-CT. Quantitative measurements of the size, CT attenuation of thymic cysts and CT attenuation of adjacent large vessels were performed on preoperative CE-CT. According to the absolute change in attenuation of the cysts between contrast-enhanced and nonenhanced CT, the patients were classified into the groups of artifactual hyper-density, unchanged density, and artifactual hypo-density. CT characteristics were compared between the three groups. Furthermore, multivariable logistic regression analysis was performed to determine the independent factors for artifactual hyper-density.ResultsThe group of artifactual hyper-density had smaller short diameter of the cysts, higher postcontrast attenuation values and lower nonenhanced attenuation values of the adjacent large vessel. Furthermore, the multivariable logistic analysis showed that artifactual hyper-density of thymic cysts was negatively associated with nonenhanced attenuation of adjacent large vessel, and positively associated with postcontrast attenuation of adjacent large vessel and postcontrast attenuation of cysts.ConclusionsMost cases with &gt;20 HU nonenhanced CT attenuation in surgically resected cases. Artifactual hyper-density─pseudo-enhancement phenomenon of thymic cysts was more apparent in higher increasing attenuation of adjacent large vessels on CE-CT. A well understanding of this phenomenon can help reduce preoperative misdiagnosis and unnecessary thymectomy.
Acute necrotizing encephalopathy associated with lymphoma-associated hemophagocytic lymphohistiocytosis: A case report and literature review
Authors: Sun Wenqiang , Fu Changchang , Zhu Xueping 
Published: October 2022

Damage associated with lymphoma-associated hemophagocytic lymphohistiocytosis (LA-HLH) to the central nervous system (CNS) is not uncommon. However, the combination with brain damage resembling acute necrotizing encephalopathy (ANE) is rarely reported. Herein, we introduce the diagnosis and treatment of a case of ANE associated with LA-HLH in our hospital and review the relevant literature. After treatment, the child was discharged with only dysarthria and decreased sucking ability. The child is now discharged from the hospital for 6 months with regular follow-up. There were no disease recurrence signs. LA-HLH and ANE were related to cytokine storm. Therefore, early steroid application is essential for treating these diseases.
Viscum album mother tinctures: Harvest conditions and host trees influence the plant metabolome and the glycolytic pathway of breast cancer cells
Authors: Melo Michelle Nonato de Oliveira , Ochioni Alan Clavelland , Zancan Patricia , Oliveira Adriana Passos , Grazi Mirio , Garrett Rafael , Holandino Carla , Baumgartner Stephan 
Published: October 2022

Viscum album is a semi-parasitic plant used for over one hundred years in complementary cancer therapy. The main commercial drugs used in cancer patients’ treatment are derived from the aqueous V. album extracts, whose cytotoxic potential is mostly attributed to the aqueous soluble antitumoral metabolites. On the counterpart, ethanol solvents must be used to obtain V. album mother tinctures. This methodology permits better solubilization of phenolic compounds, among others, which present antitumoral bioactivity. Recently, the metabolomics approach revealed the influence of the host tree on the V. album subspecies differentiation. To increase the scientific information about the chemical differences related to the host trees and to clarify the seasonal influences, in this study, the metabolome of 50 V. album mother tinctures from three subspecies (abietis, album, austriacum) and five host trees (Malus domestica, Quercus sp., Ulmus carpinifolia, Pinus sylvestris, Abies alba) was evaluated using summer and winter plant harvests. The in vitro cytotoxic activities were investigated in breast cancer cells (MDA-MB-231) and immortalized normal human keratinocytes (HaCaT). The summer V. album mother tinctures presented higher cytotoxic activity than winter ones. Among the summer samples, those prepared with V. album subsp. album were more cytotoxic than V. album subsp. abietis and subsp. V. album subsp. austriacum. The V. album harvested from Quercus petraea and Abies alba inhibited the key-glycolytic enzymes: hexokinase (HK), phosphofructokinase (PFK), pyruvate kinase (PK). This activity was related to a reduction in glucose uptake and lactate production, which were host-tree-time-dose-dependent. The untargeted metabolomic approach was able to discriminate the mother tinctures according to respective botanical classes and harvest season. A total of 188 metabolites were annotated under positive and negative modes. Fourteen compounds were responsible for the samples differentiation, and, to the best of our knowledge, eight were described in the Viscum album species for the first time. Our study shows the interruption of the Warburg effect as a novel antitumoral mechanism triggered by V. album mother tinctures, which is related to their metabolite profile. These results bring scientific evidence that encourages the use of V. album mother tinctures as a natural product for cancer therapy.
Anxiolytic effect of YangshenDingzhi granules: Integrated network pharmacology and hippocampal metabolomics
Authors: Lv Shimeng , Dai Weibo , Zheng Yan , Dong Ping , Yu Yihong , Zhao Yifan , Sun Shiguang , Bi Dezhong , Liu Chuanguo , Han Fabin , Wu Jibiao , Zhao Tingting , Ma Yuexiang , Zheng Feng , Sun Peng 
Published: October 2022

Anxiety disorder is one of the most common mental diseases. It is mainly characterized by a sudden, recurring but indescribable panic, fear, tension and/or anxiety. Yangshendingzhi granules (YSDZ) are widely used in the treatment of anxiety disorders, but its active ingredients and underlying mechanisms are not yet clear. This study integrates network pharmacology and metabolomics to investigate the potential mechanism of action of YSDZ in a rat model of anxiety. First, potential active ingredients and targets were screened by network pharmacology. Then, predictions were verified by molecular docking, molecular dynamics and western blotting. Metabolomics was used to identify differential metabolites and metabolic pathways. All results were integrated for a comprehensive analysis. Network pharmacology analysis found that Carotene, β-sitosterol, quercetin, Stigmasterol, and kaempferol in YSDZ exert anxiolytic effects mainly by acting on IL1β, GABRA1, PTGS1, ESR1, and TNF targets. Molecular docking results showed that all the affinities were lower than −5 kcal/mol, and the average affinities were −7.7764 kcal/mol. Molecular dynamics simulation results showed that RMSD was lower than 2.5 A, and the overall conformational changes of proteins were small, indicating that the small molecules formed stable complexes with proteins. The results of animal experiments showed that YSDZ exerts anxiolytic effects by regulating GABRA1 and TNF-α, ameliorating pathological damage in hippocampal CA1, and regulating metabolic pathways such as thiamine, cysteine and methionine metabolism, lysine biosynthesis and degradation. Altogether, we reveal multiple mechanisms through which YSDZ exerts its anti-anxiety effects, which may provide a reference for its clinical application and drug development.
Peripheral proteomic changes after electroconvulsive seizures in a rodent model of non-response to chronic fluoxetine
Authors: Lebeau Rodolphe H. , Mendez-David Indira , Kucynski-Noyau Laura , Henry Céline , Attali David , Plaze Marion , Colle Romain , Corruble Emmanuelle , Gardier Alain M. , Gaillard Raphaël , Guilloux Jean-Philippe , David Denis J. 
Published: October 2022

Major depressive disorder (MDD) is the psychiatric disorder with the highest prevalence in the world. Pharmacological antidepressant treatment (AD), such as selective serotonin reuptake inhibitors [SSRI, i.e., fluoxetine (Flx)] is the first line of treatment for MDD. Despite its efficacy, lack of AD response occurs in numerous patients characterizing Difficult-to-treat Depression. ElectroConvulsive Therapy (ECT) is a highly effective treatment inducing rapid improvement in depressive symptoms and high remission rates of ∼50–63% in patients with pharmaco-resistant depression. Nevertheless, the need to develop reliable treatment response predictors to guide personalized AD strategies and supplement clinical observation is becoming a pressing clinical objective. Here, we propose to establish a proteomic peripheral biomarkers signature of ECT response in an anxio/depressive animal model of non-response to AD. Using an emotionality score based on the analysis complementary behavioral tests of anxiety/depression (Elevated Plus Maze, Novelty Suppressed Feeding, Splash Test), we showed that a 4-week corticosterone treatment (35 μg/ml, Cort model) in C57BL/6JRj male mice induced an anxiety/depressive-like behavior. A 28-day chronic fluoxetine treatment (Flx, 18 mg/kg/day) reduced corticosterone-induced increase in emotional behavior. A 50% decrease in emotionality score threshold before and after Flx, was used to separate Flx-responding mice (Flx-R, n = 18), or Flx non-responder mice (Flx-NR, n = 7). Then, Flx-NR mice received seven sessions of electroconvulsive seizure (ECS, equivalent to ECT in humans) and blood was collected before and after ECS treatment. Chronic ECS normalized the elevated emotionality observed in Flx-NR mice. Then, proteins were extracted from peripheral blood mononuclear cells (PBMCs) and isolated for proteomic analysis using a high-resolution MS Orbitrap. Data are available via ProteomeXchange with identifier PXD037392. The proteomic analysis revealed a signature of 33 peripheral proteins associated with response to ECS (7 down and 26 upregulated). These proteins were previously associated with mental disorders and involved in regulating pathways which participate to the depressive disorder etiology.