bluuebunny/crossref_metadata_2025_split huggingface dataset:
The CTCF/LncRNA‐PACERR complex recruits E1A binding protein p300 to induce pro‐tumour macrophages in pancreatic ductal adenocarcinoma via directly regulating PTGS2 expression
Authors: Liu Yihao , Wang Xuelong , Zhu Youwei , Cao Yizhi , Wang Liwen , Li Fanlu , Zhang Yu , Li Ying , Zhang Zhiqiang , Luo Jiaxin , Deng Xiaxing , Peng Chenghong , Wei Gang , Chen Hao , Shen Baiyong 
Published: February 2022

AbstractBackgroundTumour‐associated macrophages (TAMs) play an important role in promoting the progression of pancreatic ductal adenocarcinoma (PDAC). Here, we aimed to study the epigenetic mechanisms in regulating pro‐tumour M2‐polarised TAMs in the PDAC tumour microenvironment.MethodsThis study was conducted based on ex vivo TAMs isolated from PDAC tissues and in vitro THP1‐derived TAM model. RNA‐sequencing (RNA‐seq), assay for transposase‐accessible chromatin with sequencing and chromatin immunoprecipitation sequencing were performed to investigate gene expression, chromatin accessibility, transcription factor binding sites and histone modifications. Gene knockdown in THP1‐derived TAMs was performed with lentivirus, and the impact of THP1‐derived TAMs on invasion and metastasis ability of PDAC cells were investigated with in vitro and in vivo functional assays. RNA‐chromatin interaction was analysed by chromatin isolation through RNA purification with sequencing. RNA‐protein interaction was studied by RNA immunoprecipitation and RNA pull‐down.ResultsOur data showed that the transcription factor CTCF (CCCTC‐binding factor) was highly expressed in TAMs and predicted to be significantly enriched in hyper‐accessible chromatin regions when compared to monocytes. High infiltration of CTCF+ TAMs was significantly associated with poor prognosis in PDAC patients. Knockdown of CTCF in THP1‐derived TAMs led to the down‐regulation of specific markers for M2‐polarised TAMs, including CD206 and CD163. When THP1‐derived TAMs with CTCF knockdown, they showed a decreased ability of invasion and metastasis. Further integrative analysis of multi‐omics data revealed that prostaglandin‐endoperoxide synthase 2 (PTGS2) and PTGS2 antisense NF‐κB1 complex‐mediated expression regulator RNA (PACERR) were critical downstream targets of CTCF and positively correlated with each other, which are closely situated on a chromosome. Knockdown of PACERR exhibited a similar phenotype as observed in CTCF knockdown THP1‐derived TAMs. Moreover, PACERR could directly bind to CTCF and recruit histone acetyltransferase E1A binding protein p300 to the promoter regions of PACERR and PTGS2, thereby enhancing histone acetylation and gene transcription, promoting the M2 polarization of TAMs in PDAC.ConclusionsOur study demonstrated a novel epigenetic regulation mechanism of promoting pro‐tumour M2‐polarised TAMs in the PDAC tumour microenvironment.
ACSS3 in brown fat drives propionate catabolism and its deficiency leads to autophagy and systemic metabolic dysfunction
Authors: Jia Zhihao , Chen Xiyue , Chen Jingjuan , Zhang Lijia , Oprescu Stephanie N. , Luo Nanjian , Xiong Yan , Yue Feng , Kuang Shihuan 
Published: February 2022

AbstractPropionate is a gut microbial metabolite that has been reported to have controversial effects on metabolic health. Here we show that propionate is activated by acyl‐CoA synthetase short‐chain family member 3 (ACSS3), located on the mitochondrial inner membrane in brown adipocytes. Knockout of Acss3 gene (Acss3–/–) in mice reduces brown adipose tissue (BAT) mass but increases white adipose tissue (WAT) mass, leading to glucose intolerance and insulin resistance that are exacerbated by high‐fat diet (HFD). Intriguingly, Acss3–/– or HFD feeding significantly elevates propionate levels in BAT and serum, and propionate supplementation induces autophagy in cultured brown and white adipocytes. The elevated levels of propionate in Acss3–/– mice similarly drive adipocyte autophagy, and pharmacological inhibition of autophagy using hydroxychloroquine ameliorates obesity, hepatic steatosis and insulin resistance of the Acss3–/– mice. These results establish ACSS3 as the key enzyme for propionate metabolism and demonstrate that accumulation of propionate promotes obesity and Type 2 diabetes through triggering adipocyte autophagy.
PRKAR2A‐derived circular RNAs promote the malignant transformation of colitis and distinguish patients with colitis‐associated colorectal cancer
Authors: Wan Daiwei , Wang Sentai , Xu Zhihua , Zan Xinquan , Liu Fei , Han Ye , Jiang Min , Wu Airong , Zhi Qiaoming 
Published: February 2022

AbstractBackgroundEmerging studies have proved that colonic inflammation caused by refractory inflammatory bowel disease (IBD) can initiate the colitis‐associated cancer (CAC), but the transition from inflammation to carcinoma is still largely unknown.MethodsIn this study, mouse colitis and CAC models were established, and the RNA‐seq by circRNA microarray was employed to identify the differentially expressed circRNAs and mRNAs in different comparisons (DSS vs. NC and AOM/DSS vs. DSS). The bioinformatics analyses were used to search the common characteristics in mouse colitis and CAC.ResultsThe K‐means clustering algorithm packaged these differential expressed circRNAs into subgroup analysis, and the data strongly implied that mmu_circ_0001109 closely correlated to the pro‐inflammatory signals, while mmu_circ_0001845 was significantly associated with the Wnt signalling pathway. Our subsequent data in vivo and in vitro confirmed that mmu_circ_0001109 could exacerbate the colitis by up‐regulating the Jak‐STAT3 and NF‐kappa B signalling pathways, and mmu_circ_0001845 promoted the CAC transformation through the Wnt signalling pathway. By RNA blasting between mice and humans, the human RTEL1‐ and PRKAR2A‐derived circRNAs, which might be considered as homeotic circRNAs of mmu_circ_0001109 and mmu_circ_0001845, respectively, were identified. The clinical data revealed that RTEL1‐derived circRNAs had no clinical significance in human IBD and CAC. However, three PRKAR2A‐derived circRNAs, which had the high RNA similarities to mmu_circ_0001845, were remarkably up‐regulated in CAC tissue samples and promoted the transition from colitis to CAC.ConclusionsOur results suggested that these human PRKAR2A‐derived circRNAs could be novel candidates for distinguishing CAC patients and predicted the prognosis of CAC.
Splicing factor arginine/serine‐rich 8 promotes multiple myeloma malignancy and bone lesion through alternative splicing of CACYBP and exosome‐based cellular communication
Authors: Zhang Yuanjiao , Yu Xichao , Sun Rongze , Min Jie , Tang Xiaozhu , Lin Zigen , Xie Siyuan , Li Xinying , Lu Shengfeng , Tian Zhidan , Gu Chunyan , Teng Lesheng , Yang Ye 
Published: February 2022

AbstractBackgroundMultiple myeloma (MM) is a distinctive malignancy of plasma cell within the bone marrow (BM), of which alternative splicing factors play vital roles in the progression. Splicing factor arginine/serine‐rich 8 (SFRS8) is the exclusive factor associated with MM prognosis, however its role in MM remains undefined.MethodsThe analyses of 3‐(4,5)‐dimethylthiahiazo (‐z‐y1)‐3,5‐di‐ phenytetrazoliumromide (MTT) assay, immunohistochemistry, flow cytometry and xenograft model were performed to examine cell proliferation, cell cycle and apoptosis in SFRS8 overexpression or knockdown MM cells in vitro and in vivo. The SFRS8‐regulated alternative splicing events were identified by RNA immunoprecipitation sequencing (RIP‐seq) and validated by RIP‐qPCR and Co‐IP methods. Exosomes were extracted from the supernatant of myeloma cells by ultracentrifugation. Bone lesion was evaluated by TRAP staining in vitro and SCID/NOD‐TIBIA mouse model. A neon electroporation system was utilised to deliver siRNA through exosomes. The effect of siRNA‐loaded exosomes in vivo was evaluated by using a patient‐derived tumor xenograft (PDX) model and SCID/NOD‐TIBIA mouse model.ResultsSFRS8 was significantly upregulated in MM samples and positively associated with poor overall survival (OS) in MM patients. SFRS8 promoted MM cell proliferation in vitro and in vivo. Furthermore, calcyclin binding protein (CACYBP) was identified as the downstream target of SFRS8. Particularly, SFRS8 could reduce CACYBP isoform1 (NM_014412.3) and increase CACYBP isoform2 (NM_001007214.1) by mediating the alternative splicing of CACYBP, thereby altering the ubiquitination degradation of β‐catenin to promote MM progression. In addition, SFRS8 promoted osteoclast differentiation through exosomes in vitro and in vivo. More importantly, exosomal siRNA targeting CACYBP isoform2 inhibited tumour growth in PDX and SCID/NOD‐TIBIA mouse models.ConclusionOur findings demonstrate that targeting the SFRS8/CACYBP/β‐catenin axis may be a promising strategy for MM diagnosis and treatment.
The central role of Sphingosine kinase 1 in the development of neuroendocrine prostate cancer (NEPC): A new targeted therapy of NEPC
Authors: Lee Cheng‐Fan , Chen Yu‐An , Hernandez Elizabeth , Pong Rey‐Chen , Ma Shihong , Hofstad Mia , Kapur Payal , Zhau Haiyen , Chung Leland WK , Lai Chih‐Ho , Lin Ho , Lee Ming‐Shyue , Raj Ganesh V , Hsieh Jer‐Tsong 
Published: February 2022

AbstractBackgroundNeuroendocrine prostate cancer (NEPC) is often diagnosed as a sub‐type from the castration‐resistant prostate cancer (CRPC) recurred from the second generation of anti‐androgen treatment and is a rapidly progressive fatal disease. The molecular mechanisms underlying the trans‐differentiation from CRPC to NEPC are not fully characterized, which hampers the development of effective targeted therapy.MethodsBioinformatic analyses were conducted to determine the clinical correlation of sphingosine kinase 1 (SphK1) in CRPC progression. To investigate the transcriptional regulation SphK1 and neuroendocrine (NE) transcription factor genes, both chromosome immunoprecipitation and luciferase reporter gene assays were performed. To demonstrate the role of SphK1 in NEPC development, neurosphere assay was carried out along with several biomarkers determined by quantitative PCR and western blot. Furthermore, in vivo NEPC xenograft models and patient‐derived xenograft (PDX) model were employed to determine the effect of SphK1 inhibitors and target validation.ResultsSignificant prevalence of SphK1 in NEPC development is observed from clinical datasets. SphK1 is transcriptionally repressed by androgen receptor‐RE1‐silencing transcription factor (REST) complex. Furthermore, sphingosine 1‐phosphate produced by SphK1 can modulate REST protein turnover via MAPK signaling pathway. Also, decreased REST protein levels enhance the expression of NE markers in CRPC, enabling the transition to NEPC. Finally, specific SphK1 inhibitors can effectively inhibit the growth of NEPC tumors and block the REST protein degradation in PDX.ConclusionsSphK1 plays a central role in NEPC development, which offers a new target for this lethal cancer using clinically approved SphK1 inhibitors.
Persistent high glucose induced EPB41L4A‐AS1 inhibits glucose uptake via GCN5 mediating crotonylation and acetylation of histones and non‐histones
Authors: Liao Weijie , Xu Naihan , Zhang Haowei , Liao Weifang , Wang Yanzhi , Wang Songmao , Zhang Shikuan , Jiang Yuyang , Xie Weidong , Zhang Yaou 
Published: February 2022

AbstractBackgroundPersistent hyperglycemia decreases the sensitivity of insulin‐sensitive organs to insulin, owing to which cells fail to take up and utilize glucose, which exacerbates the progression of type 2 diabetes mellitus (T2DM). lncRNAs' abnormal expression is reported to be associated with the progression of diabetes and plays a significant role in glucose metabolism. Herein, we study the detailed mechanism underlying the functions of lncRNA EPB41L4A‐AS1in T2DM.MethodsData from GEO datasets were used to analyze the expression of EPB41L4A‐AS1 between insulin resistance or type 2 diabetes patients and the healthy people. Gene expression was evaluated by qRT‐PCR and western blotting. Glucose uptake was measured by Glucose Uptake Fluorometric Assay Kit. Glucose tolerance of mice was detected by Intraperitoneal glucose tolerance tests. Cell viability was assessed by CCK‐8 assay. The interaction between EPB41L4A‐AS1 and GCN5 was explored by RNA immunoprecipitation, RNA pull‐down and RNA‐FISH combined immunofluorescence. Oxygen consumption rate was tested by Seahorse XF Mito Stress Test.ResultsEPB41L4A‐AS1 was abnormally increased in the liver of patients with T2DM and upregulated in the muscle cells of patients with insulin resistance and in T2DM cell models. The upregulation was associated with increased TP53 expression and reduced glucose uptake. Mechanistically, through interaction with GCN5, EPB41L4A‐AS1 regulated histone H3K27 crotonylation in the GLUT4 promoter region and nonhistone PGC1β acetylation, which inhibited GLUT4 transcription and suppressed glucose uptake by muscle cells. In contrast, EPB41L4A‐AS1 binding to GCN5 enhanced H3K27 and H3K14 acetylation in the TXNIP promoter region, which activated transcription by promoting the recruitment of the transcriptional activator MLXIP. This enhanced GLUT4/2 endocytosis and further suppressed glucose uptake.ConclusionOur study first showed that the EPB41L4A‐AS1/GCN5 complex repressed glucose uptake via targeting GLUT4/2 and TXNIP by regulating histone and nonhistone acetylation or crotonylation. Since a weaker glucose uptake ability is one of the major clinical features of T2DM, the inhibition of EPB41L4A‐AS1 expression seems to be a potentially effective strategy for drug development in T2DM treatment.
Melatonergic signalling instructs transcriptional inhibition of IFNGR2 to lessen interleukin‐1β‐dependent inflammation
Authors: Xia Yaoyao , Zhang Qingzhuo , Ye Yuyi , Wu Xiaoyan , He Fang , Peng Yuanyi , Yin Yulong , Ren Wenkai 
Published: February 2022

AbstractBackgroundImmunotransmitters (e.g., neurotransmitters and neuromodulators) could orchestrate diverse immune responses; however, the elaborated mechanism by which melatonergic activation governs inflammation remains less defined.MethodsPrimary macrophages, various cell lines, and Pasteurella multocida (PmCQ2)‐infected mice were respectively used to illustrate the influence of melatonergic signalling on inflammation in vitro and in vivo. A series of methods (e.g., RNA‐seq, metabolomics, and genetic manipulation) were conducted to reveal the mechanism whereby melatonergic signalling reduces macrophage inflammation.ResultsHere, we demonstrate that melatonergic activation substantially lessens interleukin (IL)‐1β‐dependent inflammation. Treatment of macrophages with melatonin rewires metabolic program, as well as remodels signalling pathways which depends on interferon regulatory factor (IRF) 7. Mechanistically, melatonin acts via membrane receptor (MT) 1 to increase heat shock factor (Hsf) 1 expression through lowering the inactive glycogen synthase kinase (GSK3) β, thereby transcriptionally inhibiting interferon (IFN)‐γ receptor (IFNGR) 2 and ultimately causing defective canonical signalling events [Janus kinase (JAK) 1/2‐signal transducer and activator of transcription (STAT) 1‐IRF7] and lower IL‐1β production in macrophages. Moreover, we find that melatonin amplifies host protective responses to PmCQ2 infection‐induced pneumonia.ConclusionsOur conceptual framework provides potential therapeutic targets to prevent and/or treat inflammatory diseases associating with excessive IL‐1β production.
EEF2K silencing inhibits tumour progression through repressing SPP1 and synergises with BET inhibitors in melanoma
Authors: Deng Guangtong , Zeng Furong , He Yi , Meng Yu , Sun Huiyan , Su Juan , Zhao Shuang , Cheng Yan , Chen Xiang , Yin Mingzhu 
Published: February 2022

BackgroundDespite the remarkable breakthroughs achieved in the management of metastatic melanoma using immunotherapy and targeted therapies, long‐term clinical efficacy is often compromised due to dose‐limiting toxicity and innate or acquired resistance. Therefore, it is of vital importance to further explore the molecular mechanisms underlying melanoma progression and identify new targeted therapeutic approaches.MethodsThe function of eukaryotic elongation factor‐2 kinase (EEF2K) in melanoma were investigated in vitro and in vivo. RNA‐seq and chromatin immunoprecipitation (ChIP) assay were undertaken to explore the mechanisms. The antitumor effect of bromodomain and extra terminal domain (BET) inhibitors combined with cytarabine were assessed in melanoma both in vitro and in vivo.ResultsEEF2K silencing markedly attenuated the malignant phenotypes of melanoma cells, including proliferation, migration, invasion and metastasis. In contrast, EEF2K overexpression promoted melanoma cell proliferation, migration and invasion. Mechanistically, we demonstrated that EEF2K upregulates the phosphorylation of STAT3 (p‐STAT3) at Tyr705, which binds to the promoter region of SPP1 and enhances its transcription, thus facilitating melanoma progression. Transfection‐induced re‐expression of SPP1 partly negated the inhibitory effect of EEF2K silencing on melanoma, whereas inhibition of SPP1 or STAT3 significantly abolished the efficacy of EEF2K on melanoma cells. Intriguingly, EEF2K silencing combined with BET inhibitor treatment further inhibited cell proliferation and promoted apoptosis in melanoma. We further screened the US FDA‐approved antitumour drug library and identified cytarabine as a potential clinically applicable EEF2K inhibitor that could synergise with BET inhibitors in melanoma treatment.ConclusionEEF2K/p‐STAT3/SPP1 may be a novel oncogenic pathway in melanoma progression, which could be a target for novel combination therapy for melanoma.
The central role of a two‐way positive feedback pathway in molecular targeted therapies‐mediated pyroptosis in anaplastic thyroid cancer
Authors: Zhao Qiwu , Feng Haoran , Yang Zheyu , Liang Juyong , Jin Zhijian , Chen Lingxie , Zhan Ling , Xuan Ming , Yan Jiqi , Kuang Jie , Cheng Xi , Zhao Ren , Qiu Weihua 
Published: February 2022

AbstractBackgroundAnaplastic thyroid carcinoma (ATC) is one of the most aggressive tumours. We previously confirmed that apatinib has potential therapeutic effects on ATC via regulated cell death (RCD). As a newly identified RCD, pyroptosis demonstrates direct antitumour activity different from apoptosis or autophagy. Therefore, the clinical significance, regulatory role and underlying mechanisms of pyroptosis in ATC were focused on in this study.MethodsIn a phase II trial, patients with anaplastic or poorly differentiated thyroid carcinoma received apatinib 500 mg once daily. Multiple assays were implemented to evaluate the antitumour efficacy of apatinib and/or melittin in vitro and in vivo. High‐throughput sequencing was applied to analyse differential mRNAs expression in ATC cells treated by apatinib with or without melittin. In situ Hoechst 33342/PI double‐staining, LDH release assay and enzyme‐linked immunosorbent assay (ELISA) were employed to determine pyroptosis. In mechanism exploration, quantitative RT‐PCR, Western blotting and si‐RNA knocking down were executed.ResultsSeventeen patients were evaluable. Apatinib showed a promising therapeutic effect by a disease control rate (DCR) of 88.2%; however, treatment was terminated in 23.5% of patients due to intolerable toxicity. To reduce adverse events, a pyroptosis‐mediated synergistic antitumour effect of apatinib and melittin was identified in treatment of ATC in vitro and in vivo. The caspase‐1–gasdermin D (GSDMD) axis‐mediated pyroptosis was the key to extra antitumour effect of the combination of apatinib and melittin. Moreover, caspase‐3–gasdermin E (GSDME) pyroptosis pathway also functioned importantly in addition to caspase‐1–GSDMD pathway. Evidenced by in vitro and in vivo study, a two‐way positive feedback interaction was innovatively confirmed between caspase‐1–GSDMD and caspase‐3–GSDME axes.ConclusionsThrough pyroptosis mediated by caspase‐1–GSDMD and caspase‐3–GSDME axes synchronically, low‐dosage apatinib and melittin could synergistically achieve a comparable therapeutic potential with reduced AEs. More importantly, a two‐way positive feedback interaction is innovatively proposed between these two axes, which provide a new prospect of targeted therapy.
Context is key: Parasympathetic regulation in the classroom differentially predicts preschoolers’ socially competent behaviors
Authors: Darling Laura Nelson , Holochwost Steven J. , Coffman Jennifer , Propper Cathi B. , Wagner Nicholas J. 
Published: February 2022

AbstractResearch shows that children's early social competence predicts their later academic and interpersonal success. Accordingly, early childhood education programs increasingly aim to evaluate and support children's social skill development. Despite ample theoretical and empirical work demonstrating the role of the parasympathetic nervous system (PNS) in supporting neurophysiological processes that underlie social behaviors, no study has explicitly tested whether the assessment of PNS activity in childhood educational settings provides insight into children's social functioning. The current study addresses this gap by examining the influence of context‐specific PNS regulation, assessed via respiratory sinus arrhythmia (RSA), in predicting preschool children's socially competent behavior toward peers in the classroom. Results showed that: (1) RSA withdrawal (e.g., decreases relative to a baseline task) during unstructured classroom activities predicted children's socially competent behaviors during these unstructured activities but not during structured activities, whereas (2) withdrawal during structured classroom activities predicted children's socially competent behaviors during structured activities. These results indicate that PNS activity makes context‐specific contributions to children's social behaviors and highlight the importance of assessing neurophysiological regulation in context.
Light heterogeneity affects understory plant species richness in temperate forests supporting the heterogeneity–diversity hypothesis
Authors: Helbach Jan , Frey Julian , Messier Christian , Mörsdorf Martin , Scherer‐Lorenzen Michael 
Published: February 2022

AbstractOne of the most important drivers for the coexistence of plant species is the resource heterogeneity of a certain environment, and several studies in different ecosystems have supported this resource heterogeneity–diversity hypothesis. However, to date, only a few studies have measured heterogeneity of light and soil resources below forest canopies to investigate their influence on understory plant species richness. Here, we aim to determine (1) the influence of forest stand structural complexity on the heterogeneity of light and soil resources below the forest canopy and (2) whether heterogeneity of resources increases understory plant species richness. Measures of stand structural complexity were obtained through inventories and remote sensing techniques in 135 1‐ha study plots of temperate forests, established along a gradient of forest structural complexity. We measured light intensity and soil chemical properties on six 25 m² subplots on each of these 135 plots and surveyed understory vegetation. We calculated the coefficient of variation of light and soil parameters to obtain measures of resource heterogeneity and determined understory plant species richness at plot level. Spatial heterogeneity of light and of soil pH increased with higher stand structural complexity, although heterogeneity of soil pH did not increase in conditions of generally high levels of light availability. Increasing light heterogeneity was also associated with increasing understory plant species richness. However, light heterogeneity had no such effects in conditions where soil resource heterogeneity (variation in soil C:N ratios) was low. Our results support the resource heterogeneity–diversity hypothesis for temperate forest understory at the stand scale. Our results also highlight the importance of interaction effects between the heterogeneity of both light and soil resources in determining plant species richness.