bluuebunny/crossref_metadata_2025 huggingface dataset:
Construction of a Nine-MicroRNA-Based Signature to Predict the Overall Survival of Esophageal Cancer Patients
Authors: Zhang Xiaobin , He Yi , Gu Haiyong , Liu Zhichao , Li Bin , Yang Yang , Hao Jie , Hua Rong
Published: May 2021

Background

Esophageal cancer (EC) is a common malignant tumor. MicroRNAs (miRNAs) play a key role in the occurrence and metastasis and are closely related to the prognosis of EC. Therefore, it will provide a powerful tool to predict the overall survival (OS) of EC patients based on miRNAs expression in EC tissues and blood samples.

Methods

Five independent databases, TCGA, GSE106817, GSE113486, GSE122497, and GSE112264, were used to construct nine-miRna signature and nomograms for prognosis. The bioinformatics analysis was used to predict the enrichment pathways of targets.

Results

A total of 132 overexpressed miRNAs and 23 suppressed miRNAs showed significant differential expression in both EC serum and tissue samples compared with normal samples. We also showed that nine miRNAs were related to the prognosis of EC. Higher levels of miR-15a-5p, miR-92a-3p, miR-92a-1-5p, miR-590-5p, miR-324-5p, miR-25-3p, miR-181b-5p, miR-421, and miR-93-5p were correlated to the shorter survival time in patients with EC. In addition, we constructed a risk prediction model based on the levels of nine differentially expressed miRNAs (DEMs) and found that the OS time of EC patients with high-risk score was shorter than that of EC patients with low-risk score. Furthermore, our results showed that the risk prediction scores of EC samples were higher than those of normal samples. Finally, the area under the curve (AUC) was used to analyze the risk characteristics of EC and normal controls. By calculating the AUC and the calibration curve, the RNA signature showed a good performance. Bioinformatics analysis showed that nine DEMs were associated with several crucial signaling, including p53, FoxO, PI3K-Akt, HIF-1, and TORC1 signaling. Finally, 14 messenger RNAs (mRNAs) were identified as hub targets of nine miRNAs, including BTRC, SIAH1, RNF138, CDC27, NEDD4L, MKRN1, RLIM, FBXO11, RNF34, MYLIP, FBXW7, RNF4, UBE3C, and RNF111. TCGA dataset validation showed that these hub targets were significantly differently expressed in EC tissues compared with normal samples.

Conclusion

We have constructed maps and nomograms of nine-miRna risk signals associated with EC prognosis. Bioinformatics analysis revealed that nine DEMs were associated with several crucial signaling, including p53, FoxO, PI3K-Akt, HIF-1, and TORC1 signaling, in EC. We think that this study will provide clinicians with an effective decision-making tool.
Circ-MFN2 Positively Regulates the Proliferation, Metastasis, and Radioresistance of Colorectal Cancer by Regulating the miR-574-3p/IGF1R Signaling Axis
Authors: Liu Defeng , Peng Shihao , Li Yangyang , Guo Tao
Published: May 2021

Numerous studies have shown that the expression of circular RNA (circRNA) is closely related to the malignant progression of cancer. However, the role of circ-MFN2 in colorectal cancer (CRC) is unclear. Our study aims to explore the role and mechanism of circ-MFN2 in CRC progression. The relative expression levels of circ-MFN2, microRNA (miR)-574-3p and insulin-like growth factor 1 receptor (IGF1R) were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Cell viability was determined using 3-(4, 5-dimethyl-2 thiazolyl)-2, 5-diphenyl-2-H-tetrazolium bromide (MTT) assay. The colony number and radioresistance of cells were assessed using colony formation assay. Moreover, the migration and invasion of cells were measured using transwell assay. Tumor xenograft model was constructed to evaluate the effect of circ-MFN2 knockdown on CRC tumor growth. Furthermore, dual-luciferase reporter assay was used to verify the interaction between miR-574-3p and circ-MFN2 or IGF1R. In addition, the protein level of IGF1R was evaluated by western blot (WB) analysis. Circ-MFN2 expression was elevated in CRC tissues and cells. Knockdown of circ-MFN2 restrained the proliferation, migration, invasion, and radioresistance of CRC cells in vitro. Furthermore, silenced circ-MFN2 also reduced the tumor volume and weight of CRC in vivo. MiR-574-3p could be sponged by circ-MFN2, and its inhibitor reversed the suppression effect of circ-MFN2 silencing on CRC progression. Moreover, IGF1R was a target of miR-574-3p, and its overexpression reversed the inhibition effect of miR-574-3p mimic on CRC progression. In addition, circ-MFN2 could positively regulate IGF1R expression by sponging miR-574-3p. Our results revealed that circ-MFN2 promoted the proliferation, metastasis and radioresistance of CRC through regulating the miR-574-3p/IGF1R axis, suggesting that circ-MFN2 might be a novel therapeutic biomarker for CRC.
The Epithelial-Immune Crosstalk in Pulmonary Fibrosis
Authors: Planté-Bordeneuve Thomas , Pilette Charles , Froidure Antoine
Published: May 2021

Interactions between the lung epithelium and the immune system involve a tight regulation to prevent inappropriate reactions and have been connected to several pulmonary diseases. Although the distal lung epithelium and local immunity have been implicated in the pathogenesis and disease course of idiopathic pulmonary fibrosis (IPF), consequences of their abnormal interplay remain less well known. Recent data suggests a two-way process, as illustrated by the influence of epithelial-derived periplakin on the immune landscape or the effect of macrophage-derived IL-17B on epithelial cells. Additionally, damage associated molecular patterns (DAMPs), released by damaged or dying (epithelial) cells, are augmented in IPF. Next to “sterile inflammation”, pathogen-associated molecular patterns (PAMPs) are increased in IPF and have been linked with lung fibrosis, while outer membrane vesicles from bacteria are able to influence epithelial-macrophage crosstalk. Finally, the advent of high-throughput technologies such as microbiome-sequencing has allowed for the identification of a disease-specific microbial environment. In this review, we propose to discuss how the interplays between the altered distal airway and alveolar epithelium, the lung microbiome and immune cells may shape a pro-fibrotic environment. More specifically, it will highlight DAMPs-PAMPs pathways and the specificities of the IPF lung microbiome while discussing recent elements suggesting abnormal mucosal immunity in pulmonary fibrosis.
Monocarboxylate Transporter 4 Triggered Cell Pyroptosis to Aggravate Intestinal Inflammation in Inflammatory Bowel Disease
Authors: Wang Yaodong , Zhou Xiaorong , Zou Kejian , Chen Guanhua , Huang Ling , Yang Fangying , Pan Wenxu , Xu Hongwei , Xu Zhaohui , Chen Huan , Chen Jiayu , Gong Sitang , Zhou Xuan , Xu Wanfu , Zhao Junhong
Published: May 2021

NLRP3 inflammasome has emerged as a crucial regulator of inflammatory bowel disease (IBD) characterized by a chronic inflammatory disease of the gastrointestinal tract. The expression of MCT4 is significantly increased in intestinal mucosal tissue of IBD, which has been identified to regulate intestinal barrier function. However, the function of MCT4 in cell pyroptosis remained unknown. In this study, we have established a stable cell line with MCT4 overexpression in HT-29 and CaCO2 cells, respectively. Functional analysis revealed that ectopic expression of MCT4 in CaCO2 cells contributed to cell pyroptosis as evidenced by LDH assay, which is largely attributed to Caspase-1-mediated canonical pyroptosis, but not Caspase-4 and Caspase-5, leading to cleave pro-IL-1β and IL-18 into mature form and release mediated by cleaved GSDMD. Mechanically, MCT4 overexpression in HT-29 and CaCO2 cell triggered the phosphorylation of ERK1/2 and NF-κB p65, while inhibition of MCT4 by MCT inhibitor α-Cyano-4-hydroxycinnamic acid (α-CHCA) in HT-29 and CaCO2 cells led to a significant downregulation of ERK1/2 and NF-κB activity. What’s more, blockade of ERK1/2-NF-κB pathway could reverse the promotion effect of MCT4 on IL-1β expression. Importantly, both MCT4 and Caspase-1, GSDMD were significantly increased in patients with IBD, and a positive clinical correlation between MCT4 and Caspase-1 expression was observed (p < 0.001). Taken together, these findings suggested that MCT4 promoted Caspase-1-mediated canonical cell pyroptosis to aggravate intestinal inflammation in intestinal epithelial cells (IECs) through the ERK1/2-NF-κB pathway.
Nasopharyngeal Type-I Interferon for Immediately Available Prophylaxis Against Emerging Respiratory Viral Infections
Authors: Lee Amos C. , Jeong Yunjin , Lee Sumin , Jang Haewook , Zheng Allen , Kwon Sunghoon , Repine John E.
Published: May 2021

In addition to SARS-CoV-2 and its variants, emerging viruses that cause respiratory viral infections will continue to arise. Increasing evidence suggests a delayed, possibly suppressed, type 1 interferon (IFN-I) response occurs early during COVID-19 and other viral respiratory infections such as SARS and MERS. These observations prompt considering IFN-β as a prophylactic or early intervention for respiratory viral infections. A rationale for developing and testing intranasal interferon beta (IFN-β) as an immediately available intervention for new respiratory viral infections that will arise unexpectedly in the future is presented and supported by basic and clinical trial observations. IFN-β prophylaxis could limit the spread and consequences of an emerging respiratory viral infection in at-risk individuals while specific vaccines are being developed.
Case Report: A Rare Case of Autoinflammatory Phospholipase Cγ2 (PLCγ2)-Associated Antibody Deficiency and Immune Dysregulation Complicated With Gangrenous Pyoderma and Literature Review
Authors: Wu Na , Zhang Bingqing , Wang Tao , Shen Min , Zeng Xuejun
Published: May 2021

Background

Autoinflammatory phospholipase Cγ2 (PLCγ2)-associated antibody deficiency and immune dysregulation (APLAID) is a rare autoinflammatory disease caused by gain-of-function mutations in the PLCG2 gene. Here we report a rare case of APLAID patient carrying a novel heterozygous missense PLCG2 I169V mutation with gangrenous pyoderma and concomitant high serum immunoglobulin (Ig) E level.

Methods

The patient was diagnosed as APLAID and has been treated in our department. His phenotype and genotype were carefully documented and studied. We also conducted a comprehensive literature review on APLAID.

Results

A 23-year-old Chinese Han man presented with recurrent fever for 18 years and vesiculopustular rashes for 9 years, along with chronic bronchitis, leukocytosis, increased C-reactive protein, immunodeficiency and high serum IgE. Skin biopsy showed chronic inflammatory cells infiltration. A paternal heterozygous missense variant in exon 6 of the PLCG2 gene p. I169V was identified. His vesiculopustular and IgE level responded to medium dose corticosteroids. After withdrawal of steroids, he developed severe arthritis and a large deteriorating ulceration resembling pyoderma gangrenosum on the left knee. Large dose corticosteroids were suboptimal. Then he received adalimumab with satisfactory response for arthritis and skin lesion. But he got an immunodeficiency-associated lymphoproliferative disorder 2 months later. Through literature review, there were a total of 10 APLAID patients reported by six English-language publications. Vesiculopustular rashes, sinopulmonary infection and immunodeficiency were the most frequent symptoms of APLAID patients. Glucocorticoids, intravenous immunoglobulin and biologics were clinically used to treat APLAID but none of these patients had a complete recovery.

Conclusions

The rarity and diversity of APLAID make it difficult to be diagnosed. Our study reported the first case of APLAID with gangrenous pyoderma and concomitant high IgE carrying a novel PLCG2 mutation, which may expand the clinical phenotype and genotype of APLAID.
Kinetics of Abacavir-Induced Remodelling of the Major Histocompatibility Complex Class I Peptide Repertoire
Authors: Illing Patricia T. , van Hateren Andy , Darley Rachel , Croft Nathan P. , Mifsud Nicole A. , King Samuel , Kostenko Lyudmila , Bharadwaj Mandvi , McCluskey James , Elliott Tim , Purcell Anthony W.
Published: May 2021

Abacavir hypersensitivity syndrome can occur in individuals expressing the HLA-B*57:01 major histocompatibility complex class I allotype when utilising the drug abacavir as a part of their anti-retroviral regimen. The drug is known to bind within the HLA-B*57:01 antigen binding cleft, leading to the selection of novel self-peptide ligands, thus provoking life-threatening immune responses. However, the sub-cellular location of abacavir binding and the mechanics of altered peptide selection are not well understood. Here, we probed the impact of abacavir on the assembly of HLA-B*57:01 peptide complexes. We show that whilst abacavir had minimal impact on the maturation or average stability of HLA-B*57:01 molecules, abacavir was able to differentially enhance the formation, selectively decrease the dissociation, and alter tapasin loading dependency of certain HLA-B*57:01-peptide complexes. Our data reveals a spectrum of abacavir mediated effects on the immunopeptidome which reconciles the heterogeneous functional T cell data reported in the literature.
Predicting Cetacean Distributions in the Eastern North Atlantic to Support Marine Management
Authors: Correia Ana M. , Sousa-Guedes Diana , Gil Ágatha , Valente Raul , Rosso Massimiliano , Sousa-Pinto Isabel , Sillero Neftalí , Pierce Graham J.
Published: May 2021

Data on species occurrence at the scale of their distributional range and the determination of their habitat use requirements are essential to support conservation and define management plans that account for their habitat requirements. For wide-ranging species, such as cetaceans, especially considering that their marine habitats include offshore areas, collection of such data is challenging. In the absence of dedicated surveys, alternative methodologies are needed, such as the use of data collected from platforms of opportunity and modelling techniques to predict distribution in unsurveyed areas. Using 6 years of cetacean occurrence data collected along cargo ship routes between the Iberian Peninsula, northwestern African coasts and the Macaronesian islands, we developed ecological niche models to assess habitat preferences and predict suitable habitats of the eight most frequently sighted cetacean taxa in the area. Explanatory variables used for model fitting included topographic, oceanographic, detectability, geographic and seasonal features. To provide a robust habitat characterisation, along with predictions of habitat suitability, making best use of occurrence datasets, we applied two modelling techniques, GAM and Maxent, which offer complementary strengths. Coastal areas provide important habitats for common and bottlenose dophins, while other dolphin species (spotted and striped dolphins) have a more oceanic distribution. The predicted niches of Cuvier’s beaked whale and minke whales are mainly in the high seas at northern latitudes. Suitable habitats for sperm whales and pilot whales are mostly in southern areas in continental slope regions. For all the species, models indicated that areas around seamount features offer suitable habitats, likely of high relevance in oligotrophic offshore waters. As such, dedicated survey effort in such areas would facilitate development and implementation of appropriate management plans, which are currently lacking. Our models offer an important contribution to baseline knowledge of cetacean distribution at basin-scale in the region and could support the definition of priority areas, monitoring plans, and conservation measures, essential to comply with the requirements of the EU Marine Strategy Framework Directive.
Multiple Driver Impacts on Rocky Intertidal Systems: The Need for an Integrated Approach
Authors: Kunze Charlotte , Wölfelschneider Mirco , Rölfer Lena
Published: May 2021

Most intertidal rocky systems are exposed to severe tidal, diurnal, and seasonal changes in environmental parameters. In addition, they show extreme vulnerability to anthropogenic impacts. Research on multiple drivers is therefore crucial to understand the complexity of their potential interactions. Here, we first give an overview of the natural environment and impacts of climate change on rocky shore intertidal systems, and then focus on the impacts of multiple drivers. We further provide a summary of existing multiple driver studies in the literature with the aim for a better understanding of multiple driver interactions. As multiple drivers can affect rocky shore intertidal systems at different spatial and temporal scales, and the outcome of their effects are still more of an “ecological surprise,” we recommend a more widespread assessment of the environmental and biological context. We propose a new, integrated approach based on existing literature: this complements previous frameworks but with an improved understanding of co-occurring multiple driver systems of the rocky intertidal, in order to find management solutions based on accurate and informed predictions in these times of global change.
Accurate Tumor Segmentation via Octave Convolution Neural Network
Authors: Wang Bo , Yang Jingyi , Ai Jingyang , Luo Nana , An Lihua , Feng Haixia , Yang Bo , You Zheng
Published: May 2021

Three-dimensional (3D) liver tumor segmentation from Computed Tomography (CT) images is a prerequisite for computer-aided diagnosis, treatment planning, and monitoring of liver cancer. Despite many years of research, 3D liver tumor segmentation remains a challenging task. In this paper, we propose an effective and efficient method for tumor segmentation in liver CT images using encoder-decoder based octave convolution networks. Compared with other convolution networks utilizing standard convolution for feature extraction, the proposed method utilizes octave convolutions for learning multiple-spatial-frequency features, thus can better capture tumors with varying sizes and shapes. The proposed network takes advantage of a fully convolutional architecture which performs efficient end-to-end learning and inference. More importantly, we introduce a deep supervision mechanism during the learning process to combat potential optimization difficulties, and thus the model can acquire a much faster convergence rate and more powerful discrimination capability. Finally, we integrate octave convolutions into the encoder-decoder architecture of UNet, which can generate high resolution tumor segmentation in one single forward feeding without post-processing steps. Both architectures are trained on a subset of the LiTS (Liver Tumor Segmentation) Challenge. The proposed approach is shown to significantly outperform other networks in terms of various accuracy measures and processing speed.
The FRAILMar Study Protocol: Frailty in Patients With Advanced Chronic Kidney Disease Awaiting Kidney Transplantation. A Randomized Clinical Trial of Multimodal Prehabilitation
Authors: Pérez-Sáez María José , Morgado-Pérez Andrea , Faura Anna , Muñoz-Redondo Elena , Gárriz Miguel , Muns Maria Dolors , Nogués Xavier , Marco Ester , Pascual Julio
Published: May 2021

Introduction: Frailty is very frequent among patients with chronic kidney disease (CKD) who are awaiting deceased donor kidney transplantation (KT), and transplant outcomes are worsened in those frail recipients. Frailty and poor fitness powerfully predict mortality, kidney graft survival, and healthcare utilization after KT. Intervention is essential to improve survival and quality of life for frail CKD patients, regardless of their age. Studies of post-transplant physical therapy intervention have been met with limited success, in large part due to high dropout rates. A pre-transplant clinical framework for multimodal prehabilitation interventions including physical therapy, nutritional measures, and psychological support scheduled during the KT waiting list period may improve patient retention and compliance, better mitigate the effects of frailty and poor fitness after KT, and improve main outcomes in frail CKD patients.

Main Objective: To study the effectiveness, feasibility, and safety of multimodal prehabilitation (exercise, nutritional plans, psychological advice) in KT candidates.

Methods: Randomized controlled clinical trial in 38 frail and 76 non-frail KT candidates. The prehabilitation program will consist of physical exercise (24 sessions, 8 weeks), nutritional supplementation, and psychological advice. The primary endpoint will be a composite achievement of clinical and functional main outcomes in frail and non-frail KT candidates at 90 days post-transplantation. Secondary outcomes include changes in exercise capacity, physical activity, gait speed, respiratory and peripheral muscle strength, muscle size, body composition, performance in activities of daily living (basic and instrumental), anxiety and depression symptoms, and health-related quality of life. Feasibility of the intervention will be also analyzed.

Expected Results: Multimodal prehabilitation is a feasible and effective intervention to decrease bad outcomes at 90 days post-KT by 25 and 12.5% in frail and non-frail patients, respectively.

Clinical Trial Registration:clinicaltrials.gov (NCT04701398), date: 2021, January 8th (Protocol version: Frailmar_vers2).
Expanded Genomic Sampling Refines Current Understanding of the Distribution and Evolution of Sulfur Metabolisms in the Desulfobulbales
Authors: Ward Lewis M. , Bertran Emma , Johnston David T.
Published: May 2021

The reconstruction of modern and paleo-sulfur cycling relies on understanding the long-term relative contribution of its main actors; these include microbial sulfate reduction (MSR) and microbial sulfur disproportionation (MSD). However, a unifying theory is lacking for how MSR and MSD, with the same enzyme machinery and intimately linked evolutionary histories, perform two drastically different metabolisms. Here, we aim at shedding some light on the distribution, diversity, and evolutionary histories of MSR and MSD, with a focus on the Desulfobulbales as a test case. The Desulfobulbales is a diverse and widespread order of bacteria in the Desulfobacterota (formerly Deltaproteobacteria) phylum primarily composed of sulfate reducing bacteria. Recent culture- and sequence-based approaches have revealed an expanded diversity of organisms and metabolisms within this clade, including the presence of obligate and facultative sulfur disproportionators. Here, we present draft genomes of previously unsequenced species of Desulfobulbales, substantially expanding the available genomic diversity of this clade. We leverage this expanded genomic sampling to perform phylogenetic analyses, revealing an evolutionary history defined by vertical inheritance of sulfur metabolism genes with numerous convergent instances of transition from sulfate reduction to sulfur disproportionation.
HEMNMA-3D: Cryo Electron Tomography Method Based on Normal Mode Analysis to Study Continuous Conformational Variability of Macromolecular Complexes
Authors: Harastani Mohamad , Eltsov Mikhail , Leforestier Amélie , Jonic Slavica
Published: May 2021

Cryogenic electron tomography (cryo-ET) allows structural determination of biomolecules in their native environment (in situ). Its potential of providing information on the dynamics of macromolecular complexes in cells is still largely unexploited, due to the challenges of the data analysis. The crowded cell environment and continuous conformational changes of complexes make difficult disentangling the data heterogeneity. We present HEMNMA-3D, which is, to the best of our knowledge, the first method for analyzing cryo electron subtomograms in terms of continuous conformational changes of complexes. HEMNMA-3D uses a combination of elastic and rigid-body 3D-to-3D iterative alignments of a flexible 3D reference (atomic structure or electron microscopy density map) to match the conformation, orientation, and position of the complex in each subtomogram. The elastic matching combines molecular mechanics simulation (Normal Mode Analysis of the 3D reference) and experimental, subtomogram data analysis. The rigid-body alignment includes compensation for the missing wedge, due to the limited tilt angle of cryo-ET. The conformational parameters (amplitudes of normal modes) of the complexes in subtomograms obtained through the alignment are processed to visualize the distribution of conformations in a space of lower dimension (typically, 2D or 3D) referred to as space of conformations. This allows a visually interpretable insight into the dynamics of the complexes, by calculating 3D averages of subtomograms with similar conformations from selected (densest) regions and by recording movies of the 3D reference's displacement along selected trajectories through the densest regions. We describe HEMNMA-3D and show its validation using synthetic datasets. We apply HEMNMA-3D to an experimental dataset describing in situ nucleosome conformational variability. HEMNMA-3D software is available freely (open-source) as part of ContinuousFlex plugin of Scipion V3.0 (http://scipion.i2pc.es).
A Novel GH Family 20 β-N-acetylhexosaminidase With Both Chitosanase and Chitinase Activity From Aspergillus oryzae
Authors: Qu Tianle , Zhang Chunyue , Qin Zhen , Fan Liqiang , Jiang Lihua , Zhao Liming
Published: May 2021

Aminooligosaccharides possess various biological activities and can exploit wide applications in food, pharmaceutical and cosmetic industries. Commercial aminooligosaccharides are often prepared by the hydrolysis of chitin and chitosan. In this study, a novel GH family 20 β-N-acetylhexosaminidases gene named AoNagase was cloned from Aspergillus oryzae and expressed in Pichia pastoris. The purified AoNagase had maximal activity at pH 5.5 and 65°C. It exhibited good pH stability in the range of pH 6.0–7.5 and at temperatures below 50°C. AoNagase was capable of hydrolyzing not only colloidal chitosan (508.26 U/mg) but also chitin (29.78 U/mg). The kinetic parameters (Km and Vmax) of AoNagase were 1.51 mM, 1106.02 U/mg for chitosan and 0.41 mM, 40.31 U/mg for colloidal chitin. To our knowledge, AoNagase is the first GH family 20 β-N-acetylhexosaminidase capable of hydrolyzing both chitosan and chitin. AoNagase is an endo-type β-N-acetylhexosaminidases and can potentially be used for the manufacturing of aminooligosaccharides.
Impaired Adaptation and Laminar Processing of the Oddball Paradigm in the Primary Visual Cortex of Fmr1 KO Mouse
Authors: Pak Alexandr , Kissinger Samuel T. , Chubykin Alexander A.
Published: May 2021

Both adaptation and novelty detection are an integral part of sensory processing. Recent animal oddball studies have advanced our understanding of circuitry underlying contextual processing in early sensory areas. However, it is unclear how adaptation and mismatch (MM) responses depend on the tuning properties of neurons and their laminar position. Furthermore, given that reduced habituation and sensory overload are among the hallmarks of altered sensory perception in autism, we investigated how oddball processing might be altered in a mouse model of fragile X syndrome (FX). Using silicon probe recordings and a novel spatial frequency (SF) oddball paradigm, we discovered that FX mice show reduced adaptation and enhanced MM responses compared to control animals. Specifically, we found that adaptation is primarily restricted to neurons with preferred oddball SF in FX compared to WT mice. Mismatch responses, on the other hand, are enriched in the superficial layers of WT animals but are present throughout lamina in FX animals. Last, we observed altered neural dynamics in FX mice in response to stimulus omissions. Taken together, we demonstrated that reduced feature adaptation coexists with impaired laminar processing of oddball responses, which might contribute to altered sensory perception in FX syndrome and autism.
Regulatory Mechanisms of the RNA Modification m6A and Significance in Brain Function in Health and Disease
Authors: Mathoux Justine , Henshall David C. , Brennan Gary P.
Published: May 2021

RNA modifications have emerged as an additional layer of regulatory complexity governing the function of almost all species of RNA. N6-methyladenosine (m6A), the addition of methyl groups to adenine residues, is the most abundant and well understood RNA modification. The current review discusses the regulatory mechanisms governing m6A, how this influences neuronal development and function and how aberrant m6A signaling may contribute to neurological disease. M6A is known to regulate the stability of mRNA, the processing of microRNAs and function/processing of tRNAs among other roles. The development of antibodies against m6A has facilitated the application of next generation sequencing to profile methylated RNAs in both health and disease contexts, revealing the extent of this transcriptomic modification. The mechanisms by which m6A is deposited, processed, and potentially removed are increasingly understood. Writer enzymes include METTL3 and METTL14 while YTHDC1 and YTHDF1 are key reader proteins, which recognize and bind the m6A mark. Finally, FTO and ALKBH5 have been identified as potential erasers of m6A, although there in vivo activity and the dynamic nature of this modification requires further study. M6A is enriched in the brain and has emerged as a key regulator of neuronal activity and function in processes including neurodevelopment, learning and memory, synaptic plasticity, and the stress response. Changes to m6A have recently been linked with Schizophrenia and Alzheimer disease. Elucidating the functional consequences of m6A changes in these and other brain diseases may lead to novel insight into disease pathomechanisms, molecular biomarkers and novel therapeutic targets.
Down-Regulation of Inpp5e Associated With Abnormal Ciliogenesis During Embryonic Neurodevelopment Under Inositol Deficiency
Authors: Yue Huixuan , Li Shen , Qin Jiaxing , Gao Tingting , Lyu Jianjun , Liu Yu , Wang Xiuwei , Guan Zhen , Zhu Zhiqiang , Niu Bo , Zhong Rugang , Guo Jin , Wang Jianhua
Published: May 2021

The inositol polyphosphate-5-phosphatase E (Inpp5e) gene is located on chromosome 9q34.3. The enzyme it encodes mainly hydrolyzes the 5-phosphate groups of phosphatidylinositol (3,4,5)-trisphosphate (PtdIns (3,4,5) P3) and phosphatidylinositol (4,5)-bisphosphate (PtdIns (4,5)P2), which are closely related to ciliogenesis and embryonic neurodevelopment, through mechanisms that are largely unknown. Here we studied the role of Inpp5e gene in ciliogenesis during embryonic neurodevelopment using inositol-deficiency neural tube defects (NTDs) mouse and cell models. Confocal microscopy and scanning electron microscope were used to examine the number and the length of primary cilia. The dynamic changes of Inpp5e expression in embryonic murine brain tissues were observed during Embryonic Day 10.5–13.5 (E 10.5–13.5). Immunohistochemistry, western blot, polymerase chain reaction (PCR) arrays were applied to detect the expression of Inpp5e and cilia-related genes of the embryonic brain tissues in inositol deficiency NTDs mouse. Real-time quantitative PCR (RT-qPCR) was used to validate the candidate genes in cell models. The levels of inositol and PtdIns(3,4) P2 were measured using gas chromatography-mass spectrometry (GC-MS) and enzyme linked immunosorbent assay (ELISA), respectively. Our results showed that the expression levels of Inpp5e gradually decreased in the forebrain tissues of the control embryos, but no stable trend was observed in the inositol deficiency NTDs embryos. Inpp5e expression in inositol deficiency NTDs embryos was significantly decreased compared with the control tissues. The expression levels of Inpp5e gene and the PtdIns (3,4) P2 levels were also significantly decreased in the inositol deficient cell model. A reduced number and length of primary cilia were observed in NIH3T3 cells when inositol deficient. Three important cilia-related genes (Ift80, Mkks, Smo) were down-regulated significantly in the inositol-deficient NTDs mouse and cell models, and Smo was highly involved in NTDs. In summary, these findings suggested that down-regulation of Inpp5e might be associated with abnormal ciliogenesis during embryonic neurodevelopment, under conditions of inositol deficiency.
Novel Optineurin Frameshift Insertion in a Family With Frontotemporal Dementia and Parkinsonism Without Amyotrophic Lateral Sclerosis
Authors: Dominguez Jacqueline , Yu Jeryl Tan , Tan Yi Jayne , Ng Arlene , De Guzman Ma Fe , Natividad Boots , Daroy Ma Luisa , Cano Jemellee , Yu Justine , Lian Michelle M. , Zeng Li , Lim Weng Khong , Foo Jia Nee , Ng Adeline S. L.
Published: May 2021

Frontotemporal Dementia (FTD) is a common cause of Young Onset Dementia and has diverse clinical manifestations involving behavior, executive function, language and motor function, including parkinsonism. Up to 50% of FTD patients report a positive family history, supporting a strong genetic basis, particularly in cases with both FTD and amyotrophic lateral sclerosis (FTD-ALS). Mutations in three genes are associated with the majority of familial FTD (fFTD) cases - microtubule associated protein tau gene (MAPT), granulin precursor (GRN), and hexanucleotide repeat expansions in chromosome 9 open reading frame 72- SMCR8complex subunit (C9orf72) while mutations in other genes such as optineurin (OPTN) have rarely been reported. Mutations in OPTN have been reported mostly in familial and sporadic cases of ALS, or in rare cases of FTD-ALS, but not in association with pure or predominant FTD and/or parkinsonian phenotype. Here, we report for the first time, a family from the Philippines with four members harboring a novel frameshift insertion at OPTN (Chr 10:13166090 G>GA) p.Lys328GluTer11, three of whom presented with FTD-related phenotypes. Additionally, one sibling heterozygous for the frameshift insertion had a predominantly parkinsonian phenotype resembling corticobasal syndrome, but it remains to be determined if this phenotype is related to the frameshift insertion. Notably, none of the affected members showed any evidence of motor neuron disease or ALS at the time of writing, both clinically and on electrophysiological testing, expanding the phenotypic spectrum of OPTN mutations. Close follow-up of mutation carriers for the development of new clinical features and wider investigation of additional family members with further genetic analyses will be conducted to investigate the possibility of other genetic modifiers in this family which could explain phenotypic heterogeneity.
Dietary Patterns and Their Associations With the FTO and FGF21 Gene Variants Among Emirati Adults
Authors: Naja Farah , Itani Leila , Hammoudeh Sarah , Manzoor Shaista , Abbas Nada , Radwan Hadia , Saber-Ayad Maha
Published: May 2021

Purpose: To examine the dietary patterns and their associations with the FTO and FGF21 gene variants among Emirati adults.

Methods: Using a cross-sectional design, healthy adult male and female Emiratis (n = 194) were recruited from primary health care centers in Sharjah, UAE. Participants completed a 61-item semi-quantitative food frequency questionnaire. In addition, a saliva sample was obtained for the genetic analysis. Genotyping was performed for FTOrs9939609(A>T), FTOrs9930506(A>G), FGF21 rs838133 (A > G), and FGF21 rs838145 (A > G). Dietary patterns were derived using the principal component analysis. Logistic regression analyses were used to examine the association of dietary patterns with genetic variants.

Results: Three dietary patterns were identified: “Western”: consisting of fast food, sweets, and processed meat; “Traditional Emirati” rich in vegetables, traditional Emirati-mixed-dishes and whole dairy; while whole grains, low-fat dairy, and bulgur were components of the “Prudent” pattern. Subjects carrying the A allele of the FTO rs9939609 were 2.41 times more likely to adhere to the Western pattern compared to subjects with genotype TT (OR:2.41; 95%CI:1.05–5.50). Compared with subjects with A/A, those carrying the G allele of the FTO rs9930506 were more likely to follow a Western diet (OR: 2.19; 95%CI: 1.00–4.97). Participants carrying the risk allele (A) of the FGF21 rs838133 were twice more likely to adhere to the Traditional pattern as compared to subjects with genotype GG (OR: 1.9, 95%CI: 1.01–3.57).

Conclusions: The findings of this study suggested associations among specific FTO and FGF21 gene variants with dietary patterns among Emirati adults. These findings could be used to inform evidence-based targeted nutrition preventive recommendations, especially those aiming to limit intake of western type foods.
SDHB Suppresses the Tumorigenesis and Development of ccRCC by Inhibiting Glycolysis
Authors: Fang Zhiyu , Sun Qiang , Yang Huihui , Zheng Junfang
Published: May 2021

Metabolic reprogramming is the prominent feature of clear cell renal cell carcinoma (ccRCC). Succinate dehydrogenase subunit B (SDHB) is one of subunits of mitochondrial respiratory chain complex II. The loss of SDHB function is closely related with metabolic changes in kidney cancer cells. However, the role and molecular mechanism of SDHB in ccRCC occurrence and progression are still unclear. In this study, the results of bioinformatics analyses on GEO, TCGA and oncomine databases and immunohistochemistry showed that the expression level of SDHB was downregulated in ccRCC tissues. SDHB level was gradually downregulated as ccRCC stage and grade progressed. The low level of SDHB was associated with poor prognosis of ccRCC patients, especially for advanced ccRCC patients. Increased methylation levels in SDHB gene promoter led to the downregulation of SDHB level in ccRCC tissues. SDHB was correlated with many metabolism related genes and its interacting proteins were enriched in metabolic pathways. SDHB overexpression suppressed the proliferation, colony formation and migration of ccRCC cells by inhibiting aerobic glycolysis. SDHB may be a potential prognostic marker and therapeutic target for ccRCC.
Variation in the Use of Active Surveillance for Low-Risk Prostate Cancer Across US Census Regions
Authors: Al Hussein Al Awamlh Bashir , Patel Neal , Ma Xiaoyue , Calaway Adam , Ponsky Lee , Hu Jim C. , Shoag Jonathan E.
Published: May 2021

Substantial geographic variation in healthcare practices exist. Active surveillance (AS) has emerged as a critical tool in the management of men with low-risk prostate cancer. Whether there have been regional differences in adoption is largely unknown. The SEER “Prostate with Watchful Waiting Database” was used to identify patients diagnosed with localized low-risk prostate cancer and managed with AS across US census regions between 2010 and 2016. Multivariable logistic regression models were used to determine the impact of region on undergoing AS and factors associated with AS use within each US census region. Between 2010 and 2016, the proportion of men managed with AS increased from 20.8% to 55.9% in the West, 11.5% to 50.0% in Northeast, 9.9% to 43.4% in the South and 15.1% to 56.2% in Midwest (p < 0.0001). On multivariable analysis, as compared to the West, men in all regions were less likely to undergo AS (p < 0.001). Black men in the West (OR 1.36, 95%CI 1.25–1.49) and Midwest (OR 1.62, 95%CI 1.35–1.95) were more likely to undergo AS, but less likely in Northeast (OR 0.80, 95%CI 0.69–0.92). Men with higher socioeconomic status (SES) were more likely to undergo AS in the West (OR 1.47, 95%CI 1.39–1.55), Northeast (OR 1.57, 95%CI 1.36–1.81), and South (OR 1.24, 95%CI 1.13–1.37) but not in the Midwest (OR 0.85, 95%CI 0.73–0.98). We found striking regional differences in the uptake of AS according to race and SES. Geography must be taken into consideration when assessing barriers to AS use.
Recurrence Rates of Intraosseous Ameloblastoma Cases With Conservative or Aggressive Treatment: A Systematic Review and Meta-Analysis
Authors: Qiao Xue , Shi Junxiu , Liu Jiayi , Liu Jinwen , Guo Yan , Zhong Ming
Published: May 2021

Objective

This study aimed to systematically investigate and compare the post-treatment recurrence of intraosseous ameloblastoma in patients treated with conservative or aggressive approaches.

Methods

Systemic searches of PubMed, Medline, Cochrane Library, and Embase databases from inception to October 28, 2020, were conducted. Studies that aimed to evaluate the recurrence of intraosseous ameloblastoma by conservative and aggressive treatment approaches were included.

Results

A total of 20 studies with 942 ameloblastoma cases were included. Fourteen studies included patients with ameloblastoma who received conservative treatment, and 16 studies reported the overall recurrence rate for patients undergoing aggressive treatment. The pooled results indicated that the recurrence rate for aggressive treatment [0.12, 95% confidence interval (CI) = 0.09–0.16] was significantly lower than that for conservative treatment, with a recurrence rate of 0.30 (95% CI = 0.23–0.39). Similar results were obtained when stratifying the participants by the histological classification. When trying stratification analysis following the original included studies, multicystic ameloblastoma presented a much higher recurrence rate than solid and unicystic ameloblastomas.

Conclusion

These findings supported the hypothesis that aggressive treatment might lead to a lower recurrence rate than conservative treatment. More studies and meta-analyses following the new histological classification of ameloblastomas are needed to validate and support the findings.
Yap1-2 Isoform Is the Primary Mediator in TGF-β1 Induced EMT in Pancreatic Cancer
Authors: Gao Chao , Quan Mei-Yu , Chen Qian-Jie , Yang Ruo , Wu Yuanyuan , Liu Jia-Yu , Lin Zhong-Yuan , Li Xue , Cai Jue-Ting , Jiang Tian-Fang , Xu Le , Mossahebi-Mohammadi Majid , Guo Qiang , Zhang Jin-San
Published: May 2021

Pancreatic ductal adenocarcinoma (PDAC) is the most aggressive human malignancy and intrinsically resistant to conventional therapies. YAP1, as a key downstream effector of the Hippo pathway, plays an important role in tumorigenesis including PDAC. Alternative mRNA splicing of YAP1 results in at least 8 protein isoforms, which are divided into two subgroups (YAP1-1 and YAP1-2) based on the presence of either a single or double WW domains. We investigated the functions and regulatory mechanisms of YAP1-1 and YAP1-2 in PDAC cells induced by TGF-β to undergo epithelial-to-mesenchymal transition (EMT). CRISPR-Cas9 and shRNA were used to silence YAP1 expression in pancreatic cancer cells. Re-constituted lentivirus mediated overexpression of each single YAP1 isoform was generated in the parental knockout L3.6 cells. EMT was induced by treatment with TGF-β, EGF and bFGF in parental and the constructed stable cell lines. Western blot and qPCR were used to detect the expression of EMT markers. Scratch wound healing and transwell assays were used to detect cell migration. The stability and subcellular localization of YAP1 proteins were determined by Western blot analysis, immunofluorescence, as well as ubiquitination assays. We showed that TGF-β, EGF and bFGF all significantly promoted EMT in PDAC cells, which was inhibited by knockdown of YAP1 expression. Interestingly, YAP1-1 stable cells exhibited a stronger migratory ability than YAP1-2 cells under normal culture condition. However, upon TGF-β treatment, L3.6-YAP1-2 cells exhibited a stronger migratory ability than L3.6-YAP1-1 cells. Mechanistically, TGF-β treatment preferentially stabilizes YAP1-2 and enhances its nuclear localization. Furthermore, TGF-β-induced EMT and YAP1-2 activity were both blocked by inhibition of AKT signaling. Our results showed that both YAP1-1 and YAP1-2 isoforms are important mediators in the EMT process of pancreatic cancer. However, YAP1-2 is more important in mediating TGF-β-induced EMT, which requires AKT signaling.
LINC00467 Promotes Prostate Cancer Progression via M2 Macrophage Polarization and the miR-494-3p/STAT3 Axis
Authors: Jiang Hao , Deng Wen , Zhu Ke , Zeng Zhenhao , Hu Bing , Zhou Zhengtao , Xie An , Zhang Cheng , Fu Bin , Zhou Xiaochen , Wang Gongxian
Published: May 2021

Background

The long non-coding RNA LINC00467 plays a vital role in many malignancies. Nevertheless, the role of LINC00467 in prostate carcinoma (PC) is unknown. Herein, we aimed to explore the mechanism by which LINC00467 regulates PC progression.

Methods

We used bioinformatics analyses and RT-qPCR to investigate the expression of LINC00467 in PC tissues and cells. The function of LINC00467 in the progression of PC was confirmed by loss-of-function experiments. PC cell proliferation was assessed by CCK-8 and EdU assays. The cell cycle progression of PC cells was examined by flow cytometry. Moreover, Transwell assays were used to investigate the migration and invasion of PC cells. Western blot assays were used to detect the expression of factors associated with epithelial–mesenchymal transition. The interactions of LINC00467 with prostate cancer progression and M2 macrophage polarization were confirmed by RT-qPCR. The subcellular localization of LINC00467 was investigated via the fractionation of nuclear and cytoplasmic RNA. Bioinformatics data analysis was used to predict the correlation of LINC00467 expression with miR-494-3p expression. LINC00467/miR-494-3p/STAT3 interactions were identified by using a dual-luciferase reporter system. Finally, the influence of LINC00467 expression on PC progression was investigated with an in vivo nude mouse model of tumorigenesis.

Results

We established that LINC00467 expression was upregulated in PC tissues and cells. Downregulated LINC00467 expression inhibited PC cell growth, cell cycle progression, migration, and invasion. Downregulated LINC00467 expression similarly inhibited PC cell migration via M2 macrophage polarization. Western blot analysis showed that LINC00467 could regulate the STAT3 pathway. We established that LINC00467 is mainly localized to the cytoplasm. Bioinformatics analysis and rescue experiments indicated that LINC00467 promotes PC progression via the miR-494-3p/STAT3 axis. Downregulated LINC00467 expression was also able to suppress PC tumor growth in vivo.

Conclusions

Our study reveals that LINC00467 promotes prostate cancer progression via M2 macrophage polarization and the miR-494-3p/STAT3 axis.